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Statistical features of human exons and their flanking regions

M. Zhang
1998 Human Molecular Genetics  
To facilitate gene finding and for the investigation of human molecular genetics on a genome scale, we present a comprehensive survey on various statistical features of human exons.  ...  A database for eight categories (related to human genes in which coding regions are split by introns) was built from GenBank release 87.0 and analyzed by a number of methods to characterize statistical  ...  The author is grateful for referees' detailed suggestions on how to improve the manuscript.  ... 
doi:10.1093/hmg/7.5.919 pmid:9536098 fatcat:fkkpxcfz6rhxlljiganwd2evja

GC skew is a conserved property of unmethylated CpG island promoters across vertebrates

Stella R. Hartono, Ian F. Korf, Frédéric Chédin
2015 Nucleic Acids Research  
GC skew is a measure of the strand asymmetry in the distribution of guanines and cytosines.  ...  Here, we investigated the conservation of GC skew patterns in 60 sequenced chordates genomes. We report that GC skew is a conserved sequence characteristic of the CGI promoter class in vertebrates.  ...  Using a percentile plot where genes are aligned at the start of exon 1 and the first two exons and introns (when present) are normalized in size, we confirmed that the rise of GC skew at the first exon  ... 
doi:10.1093/nar/gkv811 pmid:26253743 pmcid:PMC4787789 fatcat:rbbiu5xiujay7ncxxoes25ququ


C. E. Dutton
1881 Science  
GC skew is a measure of the strand asymmetry in the distribution of guanines and cytosines.  ...  Here, we investigated the conservation of GC skew patterns in 60 sequenced chordates genomes. We report that GC skew is a conserved sequence characteristic of the CGI promoter class in vertebrates.  ...  Using a percentile plot where genes are aligned at the start of exon 1 and the first two exons and introns (when present) are normalized in size, we confirmed that the rise of GC skew at the first exon  ... 
doi:10.1126/science.os-2.66.453 pmid:17775188 fatcat:husxdlflsvd2nacufmv6xe33h4

Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome

I. G. Mollet, Claudia Ben-Dov, Daniel Felício-Silva, A. R. Grosso, Pedro Eleutério, Ruben Alves, Ray Staller, Tito Santos Silva, Maria Carmo-Fonseca
2010 Nucleic Acids Research  
Comparison of human and mouse data revealed a marked increase, in human, of splice variants incorporating novel exons and retained introns.  ...  A subset of retained introns matching small RNAs and displaying a high GC content suggests a possible coordination between splicing regulation and production of noncoding RNAs.  ...  ACKNOWLEDGEMENTS We are indebted to Juan Valca´rcel (CRG-Centre de Regulacio´Geno´mica, Barcelona, Spain) and members of his lab Britta Hartmann and Josefin Lundgren, to Samuel Aparicio (BC Cancer Agency  ... 
doi:10.1093/nar/gkq197 pmid:20385588 pmcid:PMC2919708 fatcat:yozbkei7xrhbnawqkbj6ze7eny

Whole-Genome Microarray in Arabidopsis Facilitates Global Analysis of Retained Introns

Hadas Ner-Gaon, Robert Fluhr
2006 DNA Research  
In humans, exon skipping is the most common type while intron retention is rare. In contrast, in Arabidopsis, intron retention is the most prevalent AS type ($40%).  ...  By applying a novel algorithm retained introns are detected in 8% of the transcripts examined. A sampling of 14 transcripts showed that 86% can be confirmed by RT-PCR.  ...  The gene structure includes the genomic location and sequence of each exon and intron.  ... 
doi:10.1093/dnares/dsl003 pmid:16980712 fatcat:o6ft6migufbhbfmq54tueyi6bm

Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution

Zhongming Zhao, Yun-Xin Fu, David Hewett-Emmett, Eric Boerwinkle
2003 Gene  
In genic regions, the SNP density in intronic, exonic and adjoining untranslated regions was 8.21, 5.28, and 7.51 SNPs per 10 kb, respectively.  ...  genomic sequences, and Celera's RefSNP, which includes SNPs from a variety of sources and is biased toward disease-associated genes.  ...  This work was supported by grant from the National Heart Lung and Blood Institute and the National Institute of General Medical Sciences. Z.Z. is supported by a training fellowship from the W.M.  ... 
doi:10.1016/s0378-1119(03)00670-x pmid:12909357 fatcat:gdspcel4mjayfdml6sxfqsb4uq

A Genomic Portrait of Human Microsatellite Variation

B. A. Payseur, P. Jing, R. J. Haasl
2010 Molecular biology and evolution  
We conducted a genomic survey of variation at microsatellites with at least three perfect repeats by comparing two complete genome sequences, the Human Genome Reference sequence and the sequence of J.  ...  Reductions in variation were detected at microsatellites located in introns, in untranslated regions, in coding exons, and just upstream of transcription start sites, suggesting the presence of selective  ...  This research was supported by National Institutes of Health (grant HG004498) and a Medical Education and Research Committee New Investigator grant from the University of Wisconsin School of Medicine and  ... 
doi:10.1093/molbev/msq198 pmid:20675409 pmcid:PMC3002246 fatcat:vfpuaggkr5edpcgqev2umb636i

Intronic motif pairs cooperate across exons to promote pre-mRNA splicing

Shengdong Ke, Lawrence A Chasin
2010 Genome Biology  
Results: Strongly co-occurring motifs were found to specifically reside in four intronic regions surrounding a large number of human exons.  ...  Conclusions: The exon-flanking sequence pairs identified here by genomic analysis promote exon inclusion and may play a role in the exon definition step in pre-mRNA splicing.  ...  This work was supported by a grant from the NIH (GM072740) to LAC. Authors' contributions SK and LC conceived and planned the research, analyzed the data and wrote the manuscript.  ... 
doi:10.1186/gb-2010-11-8-r84 pmid:20704715 pmcid:PMC2945786 fatcat:kdwcm3llcnhrpamjoafyn3srji

Recombination Has Little Effect on the Rate of Sequence Divergence in Pseudoautosomal Boundary 1 Among Humans and Great Apes

S. Yi
2003 Genome Research  
In terms of base composition, although the intergenic regions of the human PAR1 show a significant increase of G and C nucleotides, the base composition of the surveyed PAR1 introns is similar to that  ...  GC content.  ...  The first four exons of this gene lie within PAR1, whereas the remaining nine exons are X-specific.  ... 
doi:10.1101/gr.1777204 pmid:14672979 pmcid:PMC314274 fatcat:4pl2ejhylzgqdlunnopuq2hx2e

Evidence of selectively driven codon usage in rice: Implications for GC content evolution ofGramineaegenes

Xingyi Guo, Jiandong Bao, Longjiang Fan
2007 FEBS Letters  
This represents a potential evolutionary process for the origin of genes with a high GC content in rice and other cereals.  ...  We used paralogs with high and low GC contents in rice and found: (a) a greater increase in GC content at exonic fourfold-redundant sites than at flanking introns; (b) with reference to their orthologs  ...  High-GC genes are shaded. Fig. 3 . Relationship between the variation in GC content at degenerate sites of exons and introns in rice.  ... 
doi:10.1016/j.febslet.2007.01.088 pmid:17306258 fatcat:oh3hany2vzah5a5dnhaa3hkmke

A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

S. Saxonov, P. Berg, D. L. Brutlag
2006 Proceedings of the National Academy of Sciences of the United States of America  
Here we adopt a direct and comprehensive survey to identify the locations of all CpGs in the human genome and find that promoters segregate naturally into two classes by CpG content.  ...  A striking feature of the human genome is the dearth of CpG dinucleotides (CpGs) interrupted occasionally by CpG islands (CGIs), regions with relatively high content of the dinucleotide.  ...  Naughton, and I. Yeh for helpful comments on the manuscript. S.S was supported by a National Library of Medicine graduate fellowship.  ... 
doi:10.1073/pnas.0510310103 pmid:16432200 pmcid:PMC1345710 fatcat:olympthlerfstkhctnrd5hienu

Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X

D. K. Nguyen, F. Yang, R. Kaul, C. Alkan, A. Antonellis, K. F. Friery, B. Zhu, P. J. de Jong, C. M. Disteche
2011 Genome Research  
Genome-wide analyses showed an overall enrichment in AT motifs unique to the eutherian X (except for genes that escape X inactivation), suggesting a role for these motifs in regulation of the X chromosome  ...  We sequenced Clcn4-2 in M. spretus and identified the breakpoints of the evolutionary translocation in the Mus lineage.  ...  BAC library construction was funded by NIH grants HG01165-07SI and HG025323-01 (P.J.d.J.) as part of the NIH-funded BAC Resource Network ( page.cfm?pageID=10001844).  ... 
doi:10.1101/gr.108563.110 pmid:21282478 pmcid:PMC3044854 fatcat:tcqizcggnbgrtlumrvzjeyzmea

Normal and abnormal mechanisms of gene splicing and relevance to inherited skin diseases

2005 Journal of dermatological science (Amsterdam)  
These regions contain well-conserved motifs which allow the splicing process to proceed in a regulated and structured manner.  ...  This review article examines the process of normal intron-exon splicing, as well as what is known about alternative splicing of human genes.  ...  Acknowledgements Funding for this work from the Dystrophic Epidermolysis Bullosa Research Association (DebRA UK) and the Royal Thai Government is gratefully acknowledged.  ... 
doi:10.1016/j.jdermsci.2005.05.006 pmid:16054339 pmcid:PMC1351063 fatcat:pdfm75k7izfntcvqmiulx2oaj4

Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture

Xavier Grau-Bové, Iñaki Ruiz-Trillo, Manuel Irimia
2018 Genome Biology  
Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes.  ...  Conclusion: We suggest that the increase of exon skipping rates in animals followed a two-step process. First, exon skipping in early animals became enriched for frame-preserving events.  ...  Roy, Arnau Sebé-Pedrós, Alexandre de Mendoza, David López-Escardó, and Nick Brown for the discussion and insightful comments they provided for this study.  ... 
doi:10.1186/s13059-018-1499-9 pmid:30223879 pmcid:PMC6142364 fatcat:ufig63zwgvanllvtugik5vgzsm

Aberrantly splicedHTT,a new player in Huntington's disease pathogenesis

Theresa A Gipson, Andreas Neueder, Nancy S Wexler, Gillian P Bates, David Housman
2013 RNA Biology  
We demonstrated that mis-splicing of mutant huntingtin intron 1 does indeed occur and results in a short polyadenylated mRNA, which is translated into an exon 1 protein.  ...  The exon 1 protein fragment is highly pathogenic. Transgenic mouse models containing just human huntingtin exon 1 develop a rapid onset of HD-like symptoms.  ...  The investigation of HTT mis-splicing was supported by Grant G0801314 from the Medical Research Council, a grant from the CHDI Foundation, and the Koch Institute Support (core) Grant P30-CA14051from the  ... 
doi:10.4161/rna.26706 pmid:24256709 pmcid:PMC3907474 fatcat:of7xg76ddfasrbqj3qp3rlrlvu
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