12864_2008_1659_MOESM3_ESM
... sequence similarity, we assume that YWHAB spawned the retrogene YWHAH. The latter covers all of the exons (no corresponding introns) of the parent gene and has been preserved from fish to mammals. After the retroposition event, YWHAG probably was derived from YWHAH, or vice versa, by segmental dupli ...
... sequence similarity, we assume that YWHAB spawned the retrogene YWHAH. The latter covers all of the exons (no corresponding introns) of the parent gene and has been preserved from fish to mammals. After the retroposition event, YWHAG probably was derived from YWHAH, or vice versa, by segmental dupli ...
Correlations Between Gene Expression and Gene Conservation in
... 1, the following analyses do not consider absolute levels of gene expression, but are based on relative expression levels (meiotic vs. vegetative expression). We found that genes induced during sexual differentiation were enriched for pombe-specific genes (Fig. 2A; Table 2). Although pombe-specific ...
... 1, the following analyses do not consider absolute levels of gene expression, but are based on relative expression levels (meiotic vs. vegetative expression). We found that genes induced during sexual differentiation were enriched for pombe-specific genes (Fig. 2A; Table 2). Although pombe-specific ...
pdf
... a. 5' end label: T4 polynucleotide kinase and [γ 32P] ATP. The reaction is most efficient if the 5' phosphate is removed (by alkaline phosphatase) prior to the kinase treatment. b. 3' end label: Klenow DNA polymerase plus [α 32P] dNTP. The labeled dNTP is chosen to be complementary to the first posi ...
... a. 5' end label: T4 polynucleotide kinase and [γ 32P] ATP. The reaction is most efficient if the 5' phosphate is removed (by alkaline phosphatase) prior to the kinase treatment. b. 3' end label: Klenow DNA polymerase plus [α 32P] dNTP. The labeled dNTP is chosen to be complementary to the first posi ...
The Modest Beginnings of One Genome Project
... involved a free-living real eukaryotic organism. While defining all the essential genes in an organism seemed out of reach, I thought it possible to at least define most of the essential genes on a single chromosome, which we guessed could represent 5% of the genome. As Mortimer and Hawthorne (1966a, ...
... involved a free-living real eukaryotic organism. While defining all the essential genes in an organism seemed out of reach, I thought it possible to at least define most of the essential genes on a single chromosome, which we guessed could represent 5% of the genome. As Mortimer and Hawthorne (1966a, ...
RNA-seq data analysis with Chipster
... We want to find genes which are differentially expressed between two human cell lines, h1-hESC and GM12878 Illumina data from the ENCODE project • 75 b single-end reads • For the interest of time, only a small subset of reads is used • No replicates (Note: you should always have at least 3 repli ...
... We want to find genes which are differentially expressed between two human cell lines, h1-hESC and GM12878 Illumina data from the ENCODE project • 75 b single-end reads • For the interest of time, only a small subset of reads is used • No replicates (Note: you should always have at least 3 repli ...
Inheritance of Organelle DNA Sequences in a Citrus–Poncirus
... nuclear genome. Insertions of organelle DNA into the nuclear genome of plants and animals have occurred frequently over the course of evolution (reviewed by Blanchard and Lynch 2000; Blanchard and Schmidt 1995; Henze and Martin 2001; Martin and Herrmann 1998). In the land plants there are many examp ...
... nuclear genome. Insertions of organelle DNA into the nuclear genome of plants and animals have occurred frequently over the course of evolution (reviewed by Blanchard and Lynch 2000; Blanchard and Schmidt 1995; Henze and Martin 2001; Martin and Herrmann 1998). In the land plants there are many examp ...
Disruption of Individual Members of Arabidopsis Syntaxin Gene
... et al., 1999), although SYP22 also has been reported to localize to the vacuole in some cell types (Sato et al., 1997). The members of the SYP2 family are most similar to the yeast prevacuolar syntaxin Pep12p (Becherer et al., 1996) and to mammalian syntaxins 7 and 13 (which reside on various endoso ...
... et al., 1999), although SYP22 also has been reported to localize to the vacuole in some cell types (Sato et al., 1997). The members of the SYP2 family are most similar to the yeast prevacuolar syntaxin Pep12p (Becherer et al., 1996) and to mammalian syntaxins 7 and 13 (which reside on various endoso ...
reviews
... alleles retained a proportion of the activity of wild-type alleles. Different alleles had an impact on different qualitative patterns of characters, contributing to unique phenotypes. Such observations supported Hermann Joseph Muller’s famous proposal that a large array of non-null alleles exists fo ...
... alleles retained a proportion of the activity of wild-type alleles. Different alleles had an impact on different qualitative patterns of characters, contributing to unique phenotypes. Such observations supported Hermann Joseph Muller’s famous proposal that a large array of non-null alleles exists fo ...
Jane M. Carlton, , 207 (2007); DOI: 10.1126/science.1132894
... Supporting Online Material (SOM) text], augmenting previous reports of conflicting phylogenetic relationships among several enzymes (7). The putative functions of these genes are diverse, affecting various metabolic pathways (fig. S2) and strongly influencing the evolution of the T. vaginalis metabo ...
... Supporting Online Material (SOM) text], augmenting previous reports of conflicting phylogenetic relationships among several enzymes (7). The putative functions of these genes are diverse, affecting various metabolic pathways (fig. S2) and strongly influencing the evolution of the T. vaginalis metabo ...
Tandem and segmental gene duplication and
... Segmental duplication: copying of entire blocks of genes from one chromosome to another. This event leads to duplication of genes to unlinked sites, even when a segment is translocated to the same chromosome. Segmental duplications can follow whole-genome duplication events. Ectopic duplication: dup ...
... Segmental duplication: copying of entire blocks of genes from one chromosome to another. This event leads to duplication of genes to unlinked sites, even when a segment is translocated to the same chromosome. Segmental duplications can follow whole-genome duplication events. Ectopic duplication: dup ...
zChap12_140901 - Online Open Genetics
... E. coli encounters many different sugars in its environment. These sugars, such as lactose and glucose, require different enzymes for their metabolism. Three of the enzymes for lactose metabolism are grouped in the lac operon: lacZ, lacY, and lacA (Figure 12.2). LacZ encodes an enzyme called β-galac ...
... E. coli encounters many different sugars in its environment. These sugars, such as lactose and glucose, require different enzymes for their metabolism. Three of the enzymes for lactose metabolism are grouped in the lac operon: lacZ, lacY, and lacA (Figure 12.2). LacZ encodes an enzyme called β-galac ...
Sathgudi Sweet orange
... (Altschul et al., 1997). After sequence comparison checking homology all the sequences were aligned to get full length genome sequence by deleting the one of the overlapping regions between sequences. Protein coding region open reading frame (ORF) was searched by Bioedit as well as by ORF finder ava ...
... (Altschul et al., 1997). After sequence comparison checking homology all the sequences were aligned to get full length genome sequence by deleting the one of the overlapping regions between sequences. Protein coding region open reading frame (ORF) was searched by Bioedit as well as by ORF finder ava ...
Codon Bias
... each of the valine codons to be used in about equal proportions. However, this is not the case for many species. For example, analysis of genes in E. coli shows that some valine codons are used more frequently than others are. The GUU codon is used in 25%, GUC is used in 21%, GUA is used in 15%, and ...
... each of the valine codons to be used in about equal proportions. However, this is not the case for many species. For example, analysis of genes in E. coli shows that some valine codons are used more frequently than others are. The GUU codon is used in 25%, GUC is used in 21%, GUA is used in 15%, and ...
emboj7601802-sup
... duplication of the resistance cassette. The new copy of the cassette, not linked to the truncated atpB allele, could hamper the selection of mutants. Thus, to prevent gene conversion and expedite the process of homoplasmisation, the inverted repeat sequences downstream of the atpB gene were removed. ...
... duplication of the resistance cassette. The new copy of the cassette, not linked to the truncated atpB allele, could hamper the selection of mutants. Thus, to prevent gene conversion and expedite the process of homoplasmisation, the inverted repeat sequences downstream of the atpB gene were removed. ...
Chapter 1 - Bioinformatics Research Center
... sequences, looking for sequences that are similar to those already identified in other genomes (both of these procedures rely on DNA alignment and comparison algorithms such as BLAST), and applying gene-finding software that recognizes DNA features that are associated with genes, such as open readin ...
... sequences, looking for sequences that are similar to those already identified in other genomes (both of these procedures rely on DNA alignment and comparison algorithms such as BLAST), and applying gene-finding software that recognizes DNA features that are associated with genes, such as open readin ...
Influence of industrial contamination on mobile genetic elements
... detected MGEs including plasmids, transposons and integrons across a wide variety of habitats (for example, Sobecky, 1999; Smalla and Sobecky, 2002; van Elsas and Bailey, 2002; Frost et al., 2005), but rarely in a quantitative manner due to previous methodological constraints. In those studies that ...
... detected MGEs including plasmids, transposons and integrons across a wide variety of habitats (for example, Sobecky, 1999; Smalla and Sobecky, 2002; van Elsas and Bailey, 2002; Frost et al., 2005), but rarely in a quantitative manner due to previous methodological constraints. In those studies that ...
Table S1.
... Table S1 – Overview of prediction attributes 0. General remarks In order to make the attributes comparable between multiple CpG islands and windows of different sizes, most attributes are averages (or standard deviations, etc.) over the window of interest, standardized to a 1kb window. Variance stab ...
... Table S1 – Overview of prediction attributes 0. General remarks In order to make the attributes comparable between multiple CpG islands and windows of different sizes, most attributes are averages (or standard deviations, etc.) over the window of interest, standardized to a 1kb window. Variance stab ...
RNA-Mediated Programming of Developmental
... events. The highly polyploid macronucleus, which divides amitotically, is a somatic nucleus: it is responsible for all vegetative transcription but is lost shortly after sexual events, to be replaced by a new one. During development of the new macronucleus, the germ line genome is amplified from 2n ...
... events. The highly polyploid macronucleus, which divides amitotically, is a somatic nucleus: it is responsible for all vegetative transcription but is lost shortly after sexual events, to be replaced by a new one. During development of the new macronucleus, the germ line genome is amplified from 2n ...
Molecular Evolution of the CMT1A-REP Region: A Human
... 200-bp product was obtained. Sequence analysis demonstrated that in these three species, the AluSc element is absent at this locus (data not shown). The results for primers T1/D2, which amplify the telomeric boundary of the distal REP, are shown in figure 3b. Fragments of the predicted size (;580 bp ...
... 200-bp product was obtained. Sequence analysis demonstrated that in these three species, the AluSc element is absent at this locus (data not shown). The results for primers T1/D2, which amplify the telomeric boundary of the distal REP, are shown in figure 3b. Fragments of the predicted size (;580 bp ...
Tutorial: chloroplast genomes - DOGMA: Annotation of Chloroplast
... strand) as well as within the sequence. To choose a different start codon than the end of the BLAST hit, click on the link and it will change the end of the gene. The start codon for psbA is correct, so we don’t need to change it. You may also change the start and end of the gene manually by typing ...
... strand) as well as within the sequence. To choose a different start codon than the end of the BLAST hit, click on the link and it will change the end of the gene. The start codon for psbA is correct, so we don’t need to change it. You may also change the start and end of the gene manually by typing ...
Transcription
... („distal“ enhancers can be very far away) - orientation not important - often target for tissue-specific or temporal regulation ...
... („distal“ enhancers can be very far away) - orientation not important - often target for tissue-specific or temporal regulation ...
CRISPR: The Last Piece of the Genetic Puzzle
... unwanted and potentially harmful mutation. Another problem is delivering the Cas9 protein and the guide crRNA into the cells.14 However, CRISPR/Cas9 is a new technology, and new systems are being developed to overcome these challenges. Synthetic CRISPR RNA (scrRNA) uses chemically modified nucleotid ...
... unwanted and potentially harmful mutation. Another problem is delivering the Cas9 protein and the guide crRNA into the cells.14 However, CRISPR/Cas9 is a new technology, and new systems are being developed to overcome these challenges. Synthetic CRISPR RNA (scrRNA) uses chemically modified nucleotid ...
Current Microbiology
... the ORF1 was named ipdC. However, upstream of position -26 referred to the ATG start codon of the gene and downstream position 112 referred to the TAA stop codon, there is no homology detectable between the DNA sequences of strain Sp7 and strain Sp245. ORF1 is followed by an inverted repeat (positio ...
... the ORF1 was named ipdC. However, upstream of position -26 referred to the ATG start codon of the gene and downstream position 112 referred to the TAA stop codon, there is no homology detectable between the DNA sequences of strain Sp7 and strain Sp245. ORF1 is followed by an inverted repeat (positio ...
How different is anatomy?
... None of the model organism databases used standard terminology to describe biological function Drosophila sequence was imminent Largest genome sequenced at that time Two weeks, 3 dozen scientists, all new software How could we organize the annotation? ...
... None of the model organism databases used standard terminology to describe biological function Drosophila sequence was imminent Largest genome sequenced at that time Two weeks, 3 dozen scientists, all new software How could we organize the annotation? ...
access full article - Caister Academic Press
... genes and the phenotypes of representative mutants are shown in figures 1A and 1B, respectively. Initial homology determinations were performed using BLAST (Altschul et al., 1990). The product of orf1 was weakly similar (61%; 59 a.a.) to phospholipase C precursor protein (Swissprot acession number P ...
... genes and the phenotypes of representative mutants are shown in figures 1A and 1B, respectively. Initial homology determinations were performed using BLAST (Altschul et al., 1990). The product of orf1 was weakly similar (61%; 59 a.a.) to phospholipase C precursor protein (Swissprot acession number P ...
Transposable element
A transposable element (TE or transposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.TEs make up a large fraction of the C-value of eukaryotic cells. There are at least two classes of TEs: class I TEs generally function via reverse transcription, while class II TEs encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. It has been shown that TEs are important in genome function and evolution. In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.