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Untranslated Regions (2):
Recent article
Untranslated Regions
Abstract
We report the functional annotation and comparative analyses of transcriptome data sets for two eastern African cichlid species, Astatotilapia burtoni and Ophthalmotilapia ventralis, representatives of the modern haplochromines and ectodines, respectively. Nearly 647,000 expressed sequence tags were...
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PMID: 21617250
PDF is available here.
PDF is available here.
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Abstract
We therefore investigated epigenetic molecular modifications that could result in variable expression of the normal NF1 allele. To exclude confounding by DNA sequence variations, we analyzed monozygotic twin pairs with NF1 who presented with several discordant features. We fine-mapped the methylatio...
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PMID: 21142935
PDF is available here.
PDF is available here.
Pediatric Research (68)3 2010
Abstract
We used complete resequencing of SFTPC and its promoter, genotyping, and logistic regression to identify 80 single nucleotide polymorphisms (SNPs). Three promoter SNPs were statistically associated with neonatal RDS among European descent infants. To assess the transcriptional effects of these three...
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PMID: 20539253
PDF is available here.
PDF is available here.
Mucosal Immunology (3)5 2010
Abstract
Regulatory T cells (Treg) express the forkhead box p3 (Foxp3) transcription factor and suppress pathological immune responses against self and foreign antigens, including commensal microorganisms. Foxp3 has been proposed as a master key regulator for Treg, required for their differen...
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PMID: 20505662
PDF is available here.
PDF is available here.
Abstract
We compare the phylogenetic utility and patterns of molecular evolution for 3'-UTRs and introns from five unlinked loci in Galliformes (Aves). 3'-UTRs evolved at slower rates and exhibited greater spatial clustering of sites with similar evolutionary rates than associated introns, though they exhibi...
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PMID: 20398778
PDF is available here.
PDF is available here.
Abstract
We examined these three SNPs in a northern Chinese population and found an association between these polymorphisms and NSCLP in both single-marker and haplotype analyses. Our data further strengthen the conclusion that altered CRISPLD2 is associated with NSCLP susceptibility.
(c) 2010 The Authors. J...
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PMID: 20662919
PDF is available here.
PDF is available here.
Abstract
Patients with LCV had a higher prevalence of moderate and high levels of HCV-RNA viremia (P = .038) than those with NAE. However, there was no significant difference in HCV genotype between LCV and NAE groups (P = .211). LIMITATIONS: Small number of cases is a limitation. CONCLUSION: Viral load seem...
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PMID: 20462666
PDF is available here.
PDF is available here.
Abstract
The miR-152 repressed HLA-G expression but exerted no effect on JEG-3 cell invasion, and overexpression of miR-152 led to increased NK cell-mediated cytolysis in JEG-3 cells. CONCLUSION: The data indicate that miR-152 may function as an immune system enhancer through up-regulating NK cell-mediated c...
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PMID: 20430358
PDF is available here.
PDF is available here.
Modern Pathology (23)5 2010
Abstract
Tetraspanins including CD9, CD37, CD63, and CD151 are linked to cellular adhesion, cell differentiation, migration, carcinogenesis, and tumor progression. The aim of the study was to detect, quantify, and evaluate the prognostic value of these tetraspanins in Merkel cell carcinoma and to study the r...
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PMID: 20118909
PDF is available here.
PDF is available here.
Abstract
We developed a reverse transcriptase based method (RTase stop assay) to characterize quadruplex formations in guanine-rich RNAs with high sensitivity and specificity. By using the RTase stop assay, we also revealed a plausible structural polymorphism in biologically important RNAs. The RTase stop as...
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PMID: 20206514
PDF is available here.
PDF is available here.
Marine Biotechnology (12)2 2010
Abstract
In order to aid gene discovery and uncover genes responding to abiotic stressors in stress-tolerant brown algae of the genus Fucus, expressed sequence tags (ESTs) were studied in two species, Fucus serratus and Fucus vesiculosus. Clustering of over 12,000 ESTs from three libraries for heat shock/rec...
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PMID: 19609612
PDF is available here.
PDF is available here.
Molecular and Cellular Endocrinology (315)1-2 2010
Abstract
We generated an expression cassette containing 1500bp of the porcine INS 5' UTR and the 3' UTR of the bovine growth hormone gene (GH). The cassette was designed to allow easy exchange of the sequences to be expressed and easy removal of the vector backbone from the expression cassette. To evaluate t...
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PMID: 19682540
PDF is available here.
PDF is available here.
Abstract
OBJECTIVE: To study the ethylene responsive element binding protein genes of Salvia miltiorrhiza through bioinformatics and characterization of its tissue expression in regenerated plantlets. METHOD: The ethylene responsive element binding protein genes were obtained by cDNA microarray analyze. BLAS...
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PMID: 20069892
PDF is available here.
PDF is available here.
Abstract
We report that CCUG repeats both bind to and misregulate the biological functions of cytoplasmic multiprotein complexes. Two CCUG-interacting complexes were subsequently purified and analyzed. A major component of one of the complexes was found to be the 20S catalytic core complex of the proteasome....
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PMID: 19590039
PDF is available here.
PDF is available here.
Abstract
We provide direct evidence for initiation from the A site in mammalian cells and, under certain conditions, also from the P site. Initiation from the A but not the P site requires PKI. Thus, PKI structure may be dynamic, and optimal IGR IRES-mediated translation of dicistroviral RNAs may require tra...
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PMID: 19647515
PDF is available here.
PDF is available here.
Molecular Biotechnology (42)3 2009
Abstract
We performed phylogenetic analysis to discern evolutionary relationships and in silico characterization to identify elements potentially important for gene regulation. We report that murine, bovine and chimpanzee sequences are the nearest neighbors of human GARS-AIRS-GART and that endo-duplication o...
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PMID: 19301155
PDF is available here.
PDF is available here.
Abstract
12 of the 13 isolates of JEV obtained in Northwestern Yunnan were identified as genotype I, only one strain was genotype III of JEV. The 12 strains of genotype I were clustered in different branches with other isolates obtained in other parts of Yunnan province. Data from sequence analysis on E gene...
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PMID: 19957629
PDF is available here.
PDF is available here.
Nihon Arukoru Yakubutsu Igakkai zasshi = Japanese journal of alcohol studies & drug dependence (44)3 2009
Abstract
I ADH is a dimmer formed by the random association of three types of subunits (alpha, beta and gamma) encoded by ADH1A, ADH1B, and ADH1C, respectively. Different kinetic properties were reported due to polymorphisms of ADH1B Arg47His and ADHIC Ile349Val. Besides these polymorphisms in the coding reg...
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PMID: 19618839
PDF is available here.
PDF is available here.
Abstract
Our data support the concept that extensive resequencing of key candidate genes can lead to the discovery of substantial numbers of new variants. Further studies using larger independent samples are needed to confirm the association of the rs61888800 SNP with antidepressant response. TRIAL REGISTRAT...
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PMID: 19414708
PDF is available here.
PDF is available here.
Cell Cycle (8)6 2009
Abstract
We report identification of ubiquitous template design sequences (templum intentio series, templints) of human genomes common for disease-associated SNPs, microRNAs and pyknons. We demonstrate that genome-unique SNP-coding sequences associated with multiple common human disorders appear assembled fr...
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PMID: 19229130
PDF is available here.
PDF is available here.
Abstract
We examined the influence of a single immobilization stress (SIS) at 2 h and 24 h afterwards on the levels of total BDNF mRNA with each exon mRNA by quantitative real-time PCR, acetylated histone at the promoters of the BDNF gene by chromatin immunoprecipitation followed by real-time PCR, and BDNF p...
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PMID: 18544182
PDF is available here.
PDF is available here.
Developmental Biology (325)1 2009
Abstract
We studied the ligand GDF3 and found that it inhibits signaling by its co-family members, the BMPs; however, GDF3 has been described by others to have Nodal-like activity. Here, we show that GDF3 can activate Nodal signaling, but only at very high doses and only upon mRNA over-expression. In contras...
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PMID: 18823971
PDF is available here.
PDF is available here.
Biophysical Journal (96)2 2009
Abstract
We use all-atom structure-based simulations to characterize the folding, unfolding, and metabolite binding of the aptamer domain of the S-adenosylmethionine-1 (SAM-1) riboswitch. Our results suggest that folding of the nonlocal helix (P1) is rate-limiting in aptamer domain formation. Interestingly,...
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PMID: 19167285
PDF is available here.
PDF is available here.
Abstract
We discuss several major classes of expression elements that have been used for maize transformation, including promoters, introns, and untranslated regions. We also discuss several strategies for further improving transgene expression levels, such as optimization of codon usage, removal of deleteri...
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PMID: 19378011
PDF is available here.
PDF is available here.
BMC Genomics (10)1 2009
Abstract
Through a genome wide analysis, we selected 41 pairs of adjacent CNE located on various chromosomes in zebrafish and obtained their intervening, less conserved, sequence information from rainbow trout. We identified 56 distinct fragments corresponding to about 150 Kbp of sequence data that were loca...
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PMID: 19549339
PDF is available here.
PDF is available here.
BMC Bioinformatics (10 Suppl 6)suppl 6 2009
Abstract
The analysis is based on a two-stepped procedure using a sequential pattern mining algorithm. The first step searches for frequent patterns (FPs) of motifs without taking into account their spatial displacement. In the second step, frequent sequential patterns (FSPs) of spaced motifs are generated b...
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PMID: 19534751
PDF is available here.
PDF is available here.
Journal of Virology (82)23 2008
Abstract
We now report the complete nucleotide sequences of three Theiler's murine encephalomyelitis virus (TMEV) strains (TO Yale, TOB15, and Vie 415HTR) and of Vilyuisk human encephalomyelitis virus (VHEV). This information, together with the recently reported sequences of divergent theiloviruses (Theiler'...
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PMID: 18815294
PDF is available here.
PDF is available here.
Hereditas (Beijing) (30)12 2008
Abstract
PCR-RFLP was applied to analyze the polymorphism of MSTN gene UTR in 345 sheep that comprised of eleven sheep breeds, namely Texel sheep, Charolais sheep, Small-tailed Han sheep, Monggolian sheep, Ujumqin sheep, Altay Fat-rumped sheep, Hulunbeir sheep, Tashikurgan sheep, Duolang sheep, Hu sheep, and...
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PMID: 19073574
PDF is available here.
PDF is available here.
Abstract
We delineate the consensus POS-1 recognition element (PRE) required for specific recognition of its target mRNAs. The PRE is necessary but not sufficient to pattern the expression of a reporter. The PRE is distinct from sequences recognized by related proteins from both mammals and nematodes, demons...
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PMID: 18952820
PDF is available here.
PDF is available here.
Abstract
We examined the association of STX1A with autism in a trio association study using DNA samples from 249 AGRE trios with autistic probands. Only male probands were selected, since autism is more prevalent among males. The probands of 102 trios had IQ>70, and were considered as high functioning autism...
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PMID: 18593506
PDF is available here.
PDF is available here.
Abstract
Abstract
We report here that Hfp regulates alternative splicing of eIF4E-1,2 pre-mRNA during Drosophila development in a sex-independent way. Hfp RNA interference-mediated knockdown in Drosophila S2 cells reproduces the eIF4E-1,2 gene expression found in development. Interestingly, 5'UTRs of eIF4E-1a and -1b...
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PMID: 18671938
PDF is available here.
PDF is available here.
Trends in Plant Science (13)10 2008
Abstract
Riboswitches are natural RNA sensors that affect post-transcriptional processes via their capacity to bind small molecules. To date, these mRNA structures have been shown to regulate the biosynthesis of essential metabolites, including vitamins and amino acids. Although bacterial riboswitches are wi...
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PMID: 18778966
PDF is available here.
PDF is available here.
Abstract
We hypothesized that fetal genes that modify PM would be associated with fetal fitness. During PM, placental trophoblasts produce soluble fms-like tyrosine kinase 1 (sFlt1), also known as soluble VEGF receptor 1, an angiogenesis inhibitor associated with preeclampsia. Here we present a study examini...
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PMID: 18779584
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)36 2008
Abstract
We have employed antibody phage display and competitive selection techniques to generate a single-chain antibody that shows >1000-fold discrimination between G-quadruplex and duplex DNA, and furthermore >100-fold discrimination between two related intramolecular parallel DNA G-quadruplexes. The amin...
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PMID: 18702511
PDF is available here.
PDF is available here.
Abstract
We examine patterns of evolution at several classes of noncoding DNA in D. simulans and find that all noncoding DNA is subject to the action of negative selection, indicated by reduced levels of polymorphism and divergence and a skew in the frequency spectrum toward rare variants. We find that the s...
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PMID: 18515263
PDF is available here.
PDF is available here.
Abstract
We have characterized the global transcriptional response of Candida albicans to ER stresses (dithiothreitol and tunicamycin) and established the impact of the transcription factor Hac1 upon this response. Expression of C. albicans Hac1, which is the functional homologue of Saccharomyces cerevisiae...
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PMID: 18602013
PDF is available here.
PDF is available here.
Hereditas (Beijing) (30)9 2008
Abstract
These results suggest that the third codon positions, introns, 3'-untranslated regions and 3' flanking sequences may evolve similarly while first and second codon positions, 5' flanking sequences and 5' untranslated region were expected to bear more selective stress for holding their functions....
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PMID: 18779175
PDF is available here.
PDF is available here.
ChemBioChem (9)12 2008
Abstract
Nature Genetics (40)8 2008
Abstract
We have determined the high-resolution strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA-DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA-DNA hybrid to detect RNA molecules hybridized to a high-density D...
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PMID: 18641648
PDF is available here.
PDF is available here.
Clinical Nephrology (70)2 2008
Abstract
Our results suggest that the 2093T-2180C haplotype at the 3'UTR of megsin gene is associated with rapid disease progression in Korean IgAN patients. This is the reverse of the results from the Chinese IgAN patients. Further studies are strongly needed to elucidate the reasons of disparity....
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PMID: 18793525
PDF is available here.
PDF is available here.
Hereditas (Beijing) (30)8 2008
Abstract
GDF-8, IGF-I, IGF-III, IGF2R, IGFBP2, and GHR are candidate genes affecting important economic trait in chicken. The putative microRNA target sites of 3' untranslated region of these genes were identified by means of specialized algorithms (miRanda and TargetScan), and the candidate SNPs located in...
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PMID: 18779153
PDF is available here.
PDF is available here.
Abstract
We present a versatile method that generates high-quality MSAs for non-protein-coding sequences. The NcDNAlign pipeline combines pairwise BLAST alignments to create initial MSAs, which are then locally improved and trimmed. The program is optimized for speed and hence is particulary well-suited to p...
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PMID: 18511233
PDF is available here.
PDF is available here.
Virus Research (135)1 2008
Comparative full genome analysis revealed E1: A226V shift in 2007 Indian Chikungunya virus isolates.
Abstract
Our finding further substantiates the association of A226V shift in E1 gene with evolutionary success possibly due to adaptation in the mosquito vector with progression of epidemic, as observed in Reunion Island. This A226V shift which was absent in all 2006 Indian isolates, is found to be present i...
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PMID: 18384900
PDF is available here.
PDF is available here.
Abstract
We have characterized the genomic organization and tissue transcription of the chicken CAT-2 (cCAT-2) isoforms from pectoralis muscle. The primary cCAT-2 transcript is alternatively spliced within the same position of the mRNA to produce cCAT-2A and cCAT-2B isoforms that share high nucleotide homolo...
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PMID: 18495509
PDF is available here.
PDF is available here.
Abstract
We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and de...
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PMID: 18451266
PDF is available here.
PDF is available here.
Abstract
We sequenced the complete mitochondrial genome of B. plicatilis sensu strictu NH1L and found that it is composed of 2 circular chromosomes, designated mtDNA-I (11,153 bp) and mtDNA-II (12,672 bp). Hybridization to DNA isolated from mitochondria demonstrated that mtDNA-I is present at 4 times the cop...
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PMID: 18326862
PDF is available here.
PDF is available here.
Abstract
Abstract
We examined 309,278 raw EST sequencing trace files of C. reinhardtii and found that only 57% had cDNA termini that matched the expected structures specified in their cDNA library constructions while satisfying our minimum length requirement for their final clean sequences. Using GMAP, 156,963 indivi...
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PMID: 18493042
PDF is available here.
PDF is available here.
Abstract
Using simple biochemical tricks, metabolite-binding riboswitches take on gene control functions that have long been thought to be the work of protein factors. Although modern riboswitches might be the last holdouts of primitive genetic elements, some are capable of sensory and regulatory feats that...
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PMID: 18369140
PDF is available here.
PDF is available here.
Virus Research (132)1-2 2008
Abstract
The complete genome of mandarin fish Siniperca chuatsi rhabdovirus (SCRV) was cloned and sequenced. It comprises 11,545 nucleotides and contains five genes encoding the nucleoprotein N, the phosphoprotein P, the matrix protein M, the glycoprotein G, and the RNA-dependent RNA polymerase protein L. At...
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PMID: 18068257
PDF is available here.
PDF is available here.
Nature Genetics (40)3 2008
Abstract
We have analyzed the degree of population differentiation at 2.8 million Phase II HapMap single-nucleotide polymorphisms. We find that negative selection has globally reduced population differentiation at amino acid-altering mutations, particularly in disease-related genes. Conversely, positive sele...
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PMID: 18246066
PDF is available here.
PDF is available here.
Abstract
The -634G>C genotype was significantly associated with an increased risk for ONFH in dominant model with odds ratio (OR) of 1.47, 95% confidence intervals (CIs) 1.08-2.01 with P value 0.015. Further analysis stratified by sex showed that the -634G>C genotype was also significantly associated with a...
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PMID: 17698375
PDF is available here.
PDF is available here.
Sleep Medicine (9)3 2008
Abstract
No coding or variants in regulatory and intronic regions compatible with a deleterious mutation were detected. Seven polymorphisms with elevated allele frequencies in the Caucasian population did not show association with RLS in two independent case-control groups and 110 RLS families. CONCLUSION: T...
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PMID: 17644423
PDF is available here.
PDF is available here.
Biotechnology Letters (30)2 2008
Abstract
The biopharmaceuticals market is currently outperforming the pharmaceuticals market and is now valued at US$ 48 billion with an average annual growth of 19%. Behind this success is a 100-fold increase in productivities of eukaryotic expression systems. However, the productivity per cell has remained...
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PMID: 17885737
PDF is available here.
PDF is available here.
Abstract
Genomic analysis of the group B coxsackieviruses (CVB) has improved our understanding of CVB evolution, epidemiology, and pathogenesis. Comparison of capsid sequence alignments and virion structures allows correlation of capsid diversity with surface features, such as loops, the receptor canyon, and...
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PMID: 18357764
PDF is available here.
PDF is available here.
Abstract
Abstract
I and VII type collagens (with a total length of exons more than 15% of the entire size of the locus). The periods observed are similar to periods typical for the nucleosomal level of the organization of chromatin. It was shown that the sites consisting of successively arranged exons and introns for...
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PMID: 18634329
PDF is available here.
PDF is available here.
Journal of Plant Physiology (165)5 2008
Abstract
The rolA gene encoded on the Ri plasmid of Agrobacterium rhizogenes causes developmental alterations, including dwarfing characteristics in the transgenic plants. In an attempt to introduce dwarfing characteristics into apple rootstocks for breeding purposes, the rolA gene was incorporated into the...
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PMID: 17490782
PDF is available here.
PDF is available here.
Abstract
Interactions between RNA-binding proteins and cis-acting elements in the 5'- and 3'-untranslated regions (UTRs) of transcripts are responsible for regulating essential biological activities, such as mRNA localization, mRNA turnover, and translation efficiency. This chapter introduces some of the pub...
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PMID: 18369972
PDF is available here.
PDF is available here.