25 Results
for term "sites"
- Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii...To understand nuclear mRNA polyadenylation mechanisms in the model alga Chlamydomonas reinhardtii, we generated a data set of 16,952 in silico-verified poly(A) sites from EST sequencing traces based on Chlamydomonas Genome Assembly v.3.1. Analysis of this data set revealed a unique and complex polyadenylation ~~~
- Genomewide Analysis of Box C/D and Box H/ACA snoRNAs in Chlamydomonas reinhardtii Reveals an Extensive Organization Into Intronic Gene Clusters....1 billion years ago. Using the powerful small nucleolar RNA (snoRNA) mining platform to screen the C. reinhardtii genome, we identified 322 snoRNA genes grouped into 118 families. The 74 box C/D families can potentially guide methylation at 96 sites of ribosomal RNAs (rRNAs) and snRNAs, and the 44 ~~~
- Expressed Sequence Tags With cDNA Termini: Previously Overlooked Resources for Gene Annotation and Transcriptome Exploration in Chlamydomonas reinhardtii...are typically trimmed of vector fragments, insert-flanking restriction endonuclease recognition sites (restriction enzyme sites), adapter (linker) sequences, and/or poly(A)/(T) tails in current cleaning steps (e.g., Liang et al. 2006; Nagaraj et al. 2006). Unfortunately, many of such trimmed sequences represent ~~~
- The Small Ubiquitin-Like Modifier (SUMO) and SUMO-Conjugating System of Chlamydomonas reinhardtii...). The conjugating system is an ATP-dependent enzymatic cascade that takes place in three steps (E1, E2, and E3). In the first step, SUMO is activated to form a thiolester linkage with the cysteine residue of the SUMO-activating enzyme (SAE) (E1). After activation, SUMO is transferred to the active-site cysteine ~~~
- The Peroxiredoxin and Glutathione Peroxidase Families in Chlamydomonas reinhardtii...and divided into four types: 2-cys PRX, 1-cys PRX, PRX-Q, and type II PRX (PRXII). In mammals, most GPXs are selenoenzymes containing a highly reactive selenocysteine in their active site while yeast and land plants are devoid of selenoproteins but contain nonselenium GPXs. The presence of a chloroplastic 2 ~~~
- FER1 and FER2 Encoding Two Ferritin Complexes in Chlamydomonas reinhardtii Chloroplasts Are Regulated by Iron...-oxyhydroxide mineral. In animals, there are two types of chainsthe light (L) chain and the heavy (H) chain (Theil 1987). The H chain carries ferroxidase active sites that oxidize ferrous to ferric iron, a prerequisite for mineralization in the core (reviewed by Chasteen 1998). The L chain, present only in vertebrates ~~~
- The Chloroplast Protein Translocation Complexes of Chlamydomonas reinhardtii: A Bioinformatic Comparison of Toc and Tic Components in Plants, Green Algae and Red Algae.... used BlastP programs in the respective JGI databases. Searches in C. merolae used the BlastP algorithm in the genome site (http://merolae.biol.s.u-tokyo.ac.jp/blast/ blast.html).BlastP searches against cyanobacterial genomeswere simultaneously performed on the NCBI server (http://www. ncbi ~~~
- Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing...of the corresponding proteins. (Top) The chromosomal arrangement of the DCL1 and AGO1 genes, which are transcribed in divergent orientation (arrows) on linkage group II (http:// genome.jgi-psf.org/Chlre3/Chlre3.home. html). Polyadenylation sites are indicated by the stop signs. (Middle) The precursor messenger RNAs ~~~
- Genome-Based Analysis of Chlamydomonas reinhardtii Exoribonucleases and Poly(A) Polymerases Predicts Unexpected Organellar and Exosomal Features...is encoded in as-yet-unsequenced DNA, or whether CrRNPH1 and CrRRP46 together fulfill the function of the Rrp41 group, remains to be established. On the basis of inferred active site residues (Lorentzen et al. 2005), CrRNPH1 (Rrp41) is predicted to exhibit exonuclease activity, whereas Rrp46 is not ~~~
- On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes..., duplicated sequences were removed and alignments of tRNA sequences were done using the TFAM package (Ardell and Andersson 2006). Only the COVEMF program was used: this program aligns a set of sequences to an existing alignment and takes into account both primary and secondary tRNA structures. All sites ~~~