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IS: a web-site for intron statistics

E. Barta, L. Kajan, S. Pongor
2003 Bioinformatics  
A web server has been established for the statistical evaluation of introns in various taxonomic groups and the comparison of taxonomic groups in terms of intron type, length, base composition, etc.  ...  The options include the graphic analysis of splice sites and a probability test for exon-shuffling within the selected group.  ...  The statistical analysis of introns is a time-consuming task which is not included into the repertoire of the currently available intron www-sites (Croft et al., 2000; Damberger and Gutell, 1994; Lopez  ... 
doi:10.1093/bioinformatics/btg019 pmid:12611812 fatcat:jro4zzz3wzbdnbjkcp4fryc4na

DNA analysis servers: plot.it, bend.it, model.it and IS

K. Vlahovicek
2003 Nucleic Acids Research  
The options include the analysis of splice sites and a probability test for exon-shuffling.  ...  The recently established introns server allows statistical evaluation of introns in various taxonomic groups and the comparison of taxonomic groups in terms of length, base composition, intron type etc  ...  ACKNOWLEDGEMENTS The development of the web servers was partly funded by EMBnet, the European Molecular Biology Network in the framework of EU project QLRI-CT-2001-01363 and by the EU-project ORIEL (IST  ... 
doi:10.1093/nar/gkg559 pmid:12824394 pmcid:PMC168966 fatcat:2tf7flvgajgmhhqorpnwcpi2mq

FOXP2 Is Not a Major Susceptibility Gene for Autism or Specific Language Impairment

D.F. Newbury, E. Bonora, J.A. Lamb, S.E. Fisher, C.S.L. Lai, G. Baird, L. Jannoun, V. Slonims, C.M. Stott, M.J. Merricks, P.F. Bolton, A.J. Bailey (+1 others)
2002 American Journal of Human Genetics  
FOXP2 is mutated in a severe monogenic form of speech and language impairment, segregating within a single large pedigree, and is also disrupted by a translocation in an isolated case.  ...  We conclude that coding-region variants in FOXP2 do not underlie the AUTS1 linkage and that the gene is unlikely to play a role in autism or more common forms of language impairment.  ...  for WAVE Machine Web site).  ... 
doi:10.1086/339931 pmid:11894222 pmcid:PMC447606 fatcat:u2ttu37a35c4dkwvowcog3grt4

Co-transcriptional folding is encoded within RNA genes

Irmtraud M Meyer, István Miklós
2004 BMC Molecular Biology  
These findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.  ...  during co-transcriptional folding are suppressed and (2) the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged.  ...  Data All 16S rRNA, 23S rRNA as well as Group I and Group II type intron sequences with completely known secondary structures were downloaded from the Comparative RNA Web (CRW) Site [35, 36] , resulting  ... 
doi:10.1186/1471-2199-5-10 pmid:15298702 pmcid:PMC514895 fatcat:x4twumd7bncglpjmvkpymwridm

Expression of Slug Is Regulated by c-Myb and Is Required for Invasion and Bone Marrow Homing of Cancer Cells of Different Origin

Barbara Tanno, Fabiola Sesti, Vincenzo Cesi, Gianluca Bossi, Giovanna Ferrari-Amorotti, Rita Bussolari, Donatella Tirindelli, Bruno Calabretta, Giuseppe Raschellà
2010 Journal of Biological Chemistry  
Such a regulatory pathway contributes to the acquisition of invasive properties that are important for the metastatic process.  ...  We show here that in embryonic kidney, colon carcinoma, chronic myeloid leukemia-blast crisis, and in neuroblastoma cells, expression of Slug is transcriptionally regulated by c-Myb via Myb binding sites  ...  A faint band was visualized after 35 cycles using the primers for site C in intron 1. No amplification was detected utilizing the primers for site D in intron 2 even after 35 PCR cycles (Fig. 3B ).  ... 
doi:10.1074/jbc.m109.089045 pmid:20622260 pmcid:PMC2937976 fatcat:u5i7rtim6bdytojofkpyxw3v54

Stochastic alternative splicing is prevalent in mungbean (Vigna radiata)

Dani Satyawan, Moon Young Kim, Suk-Ha Lee
2016 Plant Biotechnology Journal  
These observations highlight the challenges of finding and cataloguing candidates for experimentally proven AS isoforms in a crop genome.  ...  Functional AS is probably rare: a large proportion of AS isoforms exist at very low copy per cell on average or are expressed at much lower levels than default transcripts.  ...  Acknowledgements This work was supported by a grant from the Next Generation BioGreen 21 Programme (Code No. PJ01102601), Rural Development Administration, Republic of Korea.  ... 
doi:10.1111/pbi.12600 pmid:27400146 pmcid:PMC5258860 fatcat:ixfouyjay5fw3g7ne4oaoaqkmy

Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging

Viviane Labrie, Orion J Buske, Edward Oh, Richie Jeremian, Carolyn Ptak, Giedrius Gasiūnas, Almantas Maleckas, Rūta Petereit, Aida Žvirbliene, Kęstutis Adamonis, Edita Kriukienė, Karolis Koncevičius (+9 others)
2016 Nature Structural & Molecular Biology  
A total of 46 potential off-target sites were tested in the genetically-modified mice and 172 sites were tested in the Caco-2 human cell lines (Supplementary Table 3 for regions tested and primers used  ...  Consequently, it follows that this lncRNA is a natural antisense transcript, a type of regulatory element that can be controlled by DNA modification 30 , and that is increasingly recognized to alter  ... 
doi:10.1038/nsmb.3227 pmid:27159559 pmcid:PMC4899171 fatcat:kmemmknb6bhyzbvl4wpmgytqfe

Exon Inclusion Is Dependent on Predictable Exonic Splicing Enhancers

X. H.-F. Zhang, T. Kangsamaksin, M. S. P. Chao, J. K. Banerjee, L. A. Chasin
2005 Molecular and Cellular Biology  
Each of the 22 individual PESEs or PESE clusters was disrupted by site-directed mutagenesis, usually by a single-base substitution.  ...  We have previously formulated a list of approximately 2,000 RNA octamers as putative exonic splicing enhancers (PESEs) based on a statistical comparison of human exonic and nonexonic sequences (X. H.  ...  A statistical index was computed for each possible octamer based on these two comparisons.  ... 
doi:10.1128/mcb.25.16.7323-7332.2005 pmid:16055740 pmcid:PMC1190244 fatcat:6er34myg2fh75ajvpyxb23h7ou

The SERPINE2 Gene Is Associated with Chronic Obstructive Pulmonary Disease

Dawn L. DeMeo, Thomas J. Mariani, Christoph Lange, Sorachai Srisuma, Augusto A. Litonjua, Juan C. Celedón, Stephen L. Lake, John J. Reilly, Harold A. Chapman, Brigham H. Mecham, Kathleen J. Haley, Jody S. Sylvia (+8 others)
2006 American Journal of Human Genetics  
is a proven genetic risk factor for COPD.  ...  study, suggesting that SERPINE2 is a COPD-susceptibility gene and is likely influenced by gene-by-smoking interaction.  ...  This work has been funded by National Institutes of Health (NIH) grant K08 HL072918 ( Web Resources The accession number and URLs for data presented herein are as follows:  ... 
doi:10.1086/499828 pmid:16358219 pmcid:PMC1380249 fatcat:hlc537uf7vb5blvztjf2q2kkoq

The SERPINE2 Gene Is Associated with Chronic Obstructive Pulmonary Disease

D. DeMeo
2006 Proceedings of the American Thoracic Society online  
is a proven genetic risk factor for COPD.  ...  study, suggesting that SERPINE2 is a COPD-susceptibility gene and is likely influenced by gene-by-smoking interaction.  ...  This work has been funded by National Institutes of Health (NIH) grant K08 HL072918 ( Web Resources The accession number and URLs for data presented herein are as follows:  ... 
doi:10.1513/pats.200603-070ms pmid:16921128 fatcat:dbjljd5osrcpnpayx2yu5t3lea

The oncoprotein TBX3 is controlling severity in experimental arthritis

Samra Sardar, Alish Kerr, Daniëlle Vaartjes, Emilie Riis Moltved, Edita Karosiene, Ramneek Gupta, Åsa Andersson
2019 Arthritis Research & Therapy  
models for disease.  ...  The T-box protein 3 is a transcriptional repressor essential during early embryonic development, in the formation of bone and additional organ systems, and in tumorigenesis.  ...  Acknowledgements We thank Durita Poulsen and other members of the Immunopharmacology group for technical assistance, and Mathilde Caldara, Heidi Thousgaard Jensen, and Mette Lynggaard Rådbjerg for taking  ... 
doi:10.1186/s13075-018-1797-3 pmid:30630509 pmcid:PMC6329118 fatcat:4g4j5ce3lncxhkgkdf2li4uipu

NOS3 gene intron 4 a/b polymorphism is associated with ESRD in autosomal dominant polycystic kidney disease patients

Udit Narayan Padhi, Madhubala Mulkalwar, Lakkakula Saikrishna, Henu Kumar Verma, LVKS Bhaskar
2022 Brazilian Journal of Nephrology  
Conclusions: The findings of the current meta-analysis suggest that NOS3 intron 4a/b polymorphism plays a vital role in the increasing risk of ESRD in ADPKD patients.  ...  To assess the heterogeneity of studies, we used Cochrane's Q test and the Higgins and Thompson I2 statistics.  ...  The substitution of aspartic acid for glutamate affects the domain of the oxidase enzyme that serves as a binding site for BH4 and the amino acid L-arginine.  ... 
doi:10.1590/2175-8239-jbn-2021-0089 pmid:35138322 pmcid:PMC9269174 fatcat:ftctxybw5ndhhkugpf2w66f5ym

DNA methylation is associated with transcription of Snail and Slug genes

Ying Chen, Kai Wang, Chao-Nan Qian, Richard Leach
2013 Biochemical and Biophysical Research Communications - BBRC  
In summary, based on these results, DNA methylation is one of the molecular mechanisms regulating Snail and Slug genes during EMT/MET process.  ...  We found an inverse correlation between DNA methylation of first intron regions and transcription levels of Snail and Slug genes in these EMT/METs.  ...  Statistical analysis The students` T Test was used for the statistical analysis of qPCR and luciferase reporter assays. A P-value of less than 0.05 was considered statistically significant.  ... 
doi:10.1016/j.bbrc.2012.12.034 pmid:23261445 pmcid:PMC3552036 fatcat:pmht652xdva4xkvwkeumsjr2ka

Friedelin in Maytenus ilicifolia Is Produced by Friedelin Synthase Isoforms

Thaís Alves, Tatiana Souza-Moreira, Sandro Valentini, Cleslei Zanelli, Maysa Furlan
2018 Molecules  
Friedelin is a triterpene ketone with anti-inflammatory and gastroprotective activities and it is a precursor of relevant antitumor quinonemethides.  ...  The gene sequence analysis elucidated the exon/intron structure and confirmed the presence of single nucleotide polymorphisms with four non-synonymous mutations outside the active site of the enzyme.  ...  of both sterol and triterpene molecules and it is folded in the active site of oxidosqualene cyclases (OSC) in two main conformations: chair-boat-chair or chair-chair-chair for sterol or triterpene synthesis  ... 
doi:10.3390/molecules23030700 pmid:29558378 fatcat:g6vr3n3nefbr3kc5p26ymfytuy

Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma

Daniel J. Tan, Mithun Mitra, Alec M. Chiu, Hilary A. Coller
2020 npj Genomic Medicine  
AbstractPancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with a 5-year survival rate of <8%.  ...  IR levels are lower and clinical outcome is worse in IR-1 compared with IR-2. Oncogenes were significantly enriched in the set of 262 differentially retained introns between the two IR clusters.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge all of the members of the Coller laboratory for helpful input.  ... 
doi:10.1038/s41525-020-00159-4 pmid:33311498 pmcid:PMC7733475 fatcat:2k7q7gfgtnh4zdj5ma2m6hekee
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