| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q92499 | Domain | 2 | 428 | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 | Type=Deletion;Start=98;End=113 |
| Q92499 | Domain | 2 | 428 | Note=Helicase ATP-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 | Type=Deletion;Start=1;End=128 |
| Q92499 | Domain | 70 | 247 | Note=B30.2/SPRY;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00548 | Type=Deletion;Start=98;End=113 |
| Q92499 | Domain | 70 | 247 | Note=B30.2/SPRY;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00548 | Type=Deletion;Start=1;End=128 |
| Q92499 | Domain | 493 | 681 | Note=Helicase C-terminal;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00542 | Type=Substitution;Start=630;End=740 |
| Q92499 | Region | 1 | 525 | Note=Necessary for interaction with RELA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19058135;Dbxref=PMID:19058135 | Type=Deletion;Start=98;End=113 |
| Q92499 | Region | 1 | 525 | Note=Necessary for interaction with RELA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19058135;Dbxref=PMID:19058135 | Type=Deletion;Start=1;End=128 |
| Q92499 | Region | 1 | 448 | Note=Interaction with dsRNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q91VR5 | Type=Deletion;Start=98;End=113 |
| Q92499 | Region | 1 | 448 | Note=Interaction with dsRNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q91VR5 | Type=Deletion;Start=1;End=128 |
| Q92499 | Region | 1 | 295 | Note=Necessary for interaction with HNRNPK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12183465;Dbxref=PMID:12183465 | Type=Deletion;Start=98;End=113 |
| Q92499 | Region | 1 | 295 | Note=Necessary for interaction with HNRNPK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12183465;Dbxref=PMID:12183465 | Type=Deletion;Start=1;End=128 |
| Q92499 | Region | 525 | 740 | Note=Necessary for interaction with HNRNPK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12183465;Dbxref=PMID:12183465 | Type=Substitution;Start=630;End=740 |
| Q92499 | Region | 536 | 631 | Note=Necessary for interaction with replicase polyprotein 1ab nsp14 of IBV;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20573827;Dbxref=PMID:20573827 | Type=Substitution;Start=630;End=740 |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| Q92499-1 | 1.011 | 281 | 0.913 | 798.504 | 0.497 | 0.714 | 0.994 | 0.242 | 1.397 | 0.173 | 0.74 | 37,38,39,40,41,43,63,79,80,81,82,86,87,89,90,91,92
,95,96,98,99,100,101,102,103,104,105,106,107,108,1
09,110,112,113,114,115,237,242,244,365,366,388,389
,393,394,398,399,400,401,402,403,419,420,421,422,4
23,424,425,426,428
|
| Q92499-2 | 1.016 | 87 | 0.946 | 219.177 | 0.446 | 0.795 | 1.076 | 0.357 | 1.251 | 0.285 | 1.02 | 47,48,355,392,416,420,422,560,561,562,566,567,584,
585,588,589,590,591,592
|
| Q92499-3 | 1.048 | 63 | 1.006 | 103.929 | 0.3 | 0.991 | 1.402 | 2.68 | 1.026 | 2.611 | 0.878 | 336,337,338,339,362,365,385,386,387,390,393,394,46
2,463,496,498,499
|
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q92499 | Region | 1 | 525 | Note=Necessary for interaction with RELA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19058135;Dbxref=PMID:19058135 | Type=Deletion;Start=98;End=113 |
| Q92499 | Region | 1 | 525 | Note=Necessary for interaction with RELA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19058135;Dbxref=PMID:19058135 | Type=Deletion;Start=1;End=128 |
| Q92499 | Region | 1 | 448 | Note=Interaction with dsRNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q91VR5 | Type=Deletion;Start=98;End=113 |
| Q92499 | Region | 1 | 448 | Note=Interaction with dsRNA;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q91VR5 | Type=Deletion;Start=1;End=128 |
| Q92499 | Region | 1 | 295 | Note=Necessary for interaction with HNRNPK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12183465;Dbxref=PMID:12183465 | Type=Deletion;Start=98;End=113 |
| Q92499 | Region | 1 | 295 | Note=Necessary for interaction with HNRNPK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12183465;Dbxref=PMID:12183465 | Type=Deletion;Start=1;End=128 |
| Q92499 | Region | 525 | 740 | Note=Necessary for interaction with HNRNPK;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12183465;Dbxref=PMID:12183465 | Type=Substitution;Start=630;End=740 |
| Q92499 | Region | 536 | 631 | Note=Necessary for interaction with replicase polyprotein 1ab nsp14 of IBV;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20573827;Dbxref=PMID:20573827 | Type=Substitution;Start=630;End=740 |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| DDX1 | 16230076 | Beta-catenin interacts with the FUS proto-oncogene product and regulates pre-mRNA splicing. | beta-Catenin is a downstream effector of the Wnt signaling pathway and is believed to exert its oncogenic function by activating T-cell factor (TCF)/lymphoid enhancer factor (LEF) family transcriptional factors. However, it is still uncertain whether the diverse effects of beta-catenin are caused solely by aberrant gene transactivation. In this study, we used a proteomics approach to obtain further insight into the functional properties of nuclear beta-catenin. | D015179 | Colorectal Neoplasms |
| DDX1 | 21697133 | Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. | PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina. | D019572 | Retinal Neoplasms |
| DDX1 | 21697133 | Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. | PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina. | D012175 | Retinoblastoma |
| DDX1 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D004392 | Dwarfism |
| DDX1 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D006130 | Growth Disorders |
| DDX1 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D009123 | Muscle Hypotonia |
Gene summary
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