Exercise - GEP Community Server
... c. Each of the three state paths listed above has the 5’ splice site at a different position in the sequence. Which position in the sequence has the highest probability of being the 5’ splice site? How confident are you that this position is the correct choice for the 5’ splice site? ...
... c. Each of the three state paths listed above has the 5’ splice site at a different position in the sequence. Which position in the sequence has the highest probability of being the 5’ splice site? How confident are you that this position is the correct choice for the 5’ splice site? ...
Molecular Microbial Ecology of the Rhizosphere
... 2005). In some of the FZB42T islands, additional features, such as adjacent tRNAs, remnants of phages, transposase like sequences, and direct repeats, are indicative of horizontal gene transfer (Chen et al., 2007). The approximately 150 genes only occurring in the plant-associated subspecies “planta ...
... 2005). In some of the FZB42T islands, additional features, such as adjacent tRNAs, remnants of phages, transposase like sequences, and direct repeats, are indicative of horizontal gene transfer (Chen et al., 2007). The approximately 150 genes only occurring in the plant-associated subspecies “planta ...
genes. Numbers of 6-10 copies per genome have
... The SSU genes and flanking regions in TSSU3-2 and TSSU3-8 were sequenced. Using sequences of other SSU genes, the leader peptide, mature coding regions and introns were located. In Figure 2, the sequence of these two genes is shown and compared to that of a previously sequenced tobacco SSU gene, NtS ...
... The SSU genes and flanking regions in TSSU3-2 and TSSU3-8 were sequenced. Using sequences of other SSU genes, the leader peptide, mature coding regions and introns were located. In Figure 2, the sequence of these two genes is shown and compared to that of a previously sequenced tobacco SSU gene, NtS ...
Slide 1
... Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key. Trends Genet. 2006, 22(1):5-10. ...
... Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key. Trends Genet. 2006, 22(1):5-10. ...
Discovery of Muscle Atrophy Gene Regulatory Network Using
... Brandon King Gilberto Hernandez, M.D. ...
... Brandon King Gilberto Hernandez, M.D. ...
Sc!ence - Return to Home Page
... In 1945, McClintock discovered that when corn chromosomes had broken and reattached several times, one cell would completely lose a chunk of genetic material that then showed up in another cell. She discovered that chromosomes include switches that turn genes on and off and activators that can make ...
... In 1945, McClintock discovered that when corn chromosomes had broken and reattached several times, one cell would completely lose a chunk of genetic material that then showed up in another cell. She discovered that chromosomes include switches that turn genes on and off and activators that can make ...
Detection of Large Expansions in SCA8 Using a Fluorescent Repeat
... is unable to give an accurate size of the expansion. Using this method, we were able to detect expansions (73-221) that had already been diagnosed. No controls showed pathogenic patterns. There were no false-positive or false-negative results. This method appears to be sensitive, specific, reliable, ...
... is unable to give an accurate size of the expansion. Using this method, we were able to detect expansions (73-221) that had already been diagnosed. No controls showed pathogenic patterns. There were no false-positive or false-negative results. This method appears to be sensitive, specific, reliable, ...
The percentage of bacterial genes on leading versus
... levels on the leading strand increases as the expression level (averaged over all the available experimental conditions) goes up, as shown in Fig. 1(b), which is consistent with a previous finding (4, 12) that highly expressed genes tend to be on the leading strands. ...
... levels on the leading strand increases as the expression level (averaged over all the available experimental conditions) goes up, as shown in Fig. 1(b), which is consistent with a previous finding (4, 12) that highly expressed genes tend to be on the leading strands. ...
Petunia Ap2-like Genes and Their Role in Flower and
... one of which has a higher intensity than the other two (Figure 1A). When the blot was stripped and rehybridized with a 4-kb PhAp2A genomic subclone, only the strongest hybridizing band was observed (Figure 1B). These results indicate that PhAp2A belongs to a gene family and that at least two other P ...
... one of which has a higher intensity than the other two (Figure 1A). When the blot was stripped and rehybridized with a 4-kb PhAp2A genomic subclone, only the strongest hybridizing band was observed (Figure 1B). These results indicate that PhAp2A belongs to a gene family and that at least two other P ...
Alus
... and Alus • An estimated 500-2,000 Alu elements are restricted to the human genome. The vast majority of Alu insertions occur in non-coding regions and are thought to be evolutionarily neutral. However, an Alu insertion in the NF-1 gene is responsible for neurofibromatosis I, Alu insertions in intron ...
... and Alus • An estimated 500-2,000 Alu elements are restricted to the human genome. The vast majority of Alu insertions occur in non-coding regions and are thought to be evolutionarily neutral. However, an Alu insertion in the NF-1 gene is responsible for neurofibromatosis I, Alu insertions in intron ...
CHARACTERlZATION OF THE ~ 0 CHONDRIA . L DNA MOLECULE
... each other (Desjardins and Morais, 1990; 199 1). In contrast to the vertebrates, invertebrates have undergone significant rearrangements in mtDNA gene order. Multiple inversions and translocations involving numerous loci are evident when the mtDNA genomes are compared between insects, sea urchins an ...
... each other (Desjardins and Morais, 1990; 199 1). In contrast to the vertebrates, invertebrates have undergone significant rearrangements in mtDNA gene order. Multiple inversions and translocations involving numerous loci are evident when the mtDNA genomes are compared between insects, sea urchins an ...
An In Silico Investigation Into the Discovery of Novel Cis
... Several potential cis-regulatory motifs were identified in this investigation and one in particular that was common to both PAX7 and PAX3 and also to NF1, could have implications for the role of PAX7 in Alveolar Rhabdomyosarcoma and may be the cornerstone to more exciting, unique scientific investig ...
... Several potential cis-regulatory motifs were identified in this investigation and one in particular that was common to both PAX7 and PAX3 and also to NF1, could have implications for the role of PAX7 in Alveolar Rhabdomyosarcoma and may be the cornerstone to more exciting, unique scientific investig ...
Learning objectives for Sequence Analysis 1
... 18. Following scheme is helpful for resolving of the problems of pair-wise sequence comparison: ...
... 18. Following scheme is helpful for resolving of the problems of pair-wise sequence comparison: ...
Red Line Walk-through
... sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.” http://www.ncbi.nlm.nih.gov/u nigene cDNA: DNA produced by reverse transcribing mRNA using r ...
... sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.” http://www.ncbi.nlm.nih.gov/u nigene cDNA: DNA produced by reverse transcribing mRNA using r ...
Text S1.
... Criteria to define trans-specifically shared S-alleles Based on the mismatch distribution for interspecific pairs of SRK sequences between A. lyrata and A. halleri (Fig. 2), we defined "trans-specifically shared S-alleles", i.e. alleles assumed to have evolved from a single S-allele in the direct an ...
... Criteria to define trans-specifically shared S-alleles Based on the mismatch distribution for interspecific pairs of SRK sequences between A. lyrata and A. halleri (Fig. 2), we defined "trans-specifically shared S-alleles", i.e. alleles assumed to have evolved from a single S-allele in the direct an ...
Synonymous codon bias and functional constraint on GC3
... occurring with high frequency also tend to be represented by more codons, thus facilitating degeneracy in the code that might additionally facilitate functional variation in unknown ways. While it is now clear that natural selection acts on synonymous codons (10,11), the exact molecular traits upon ...
... occurring with high frequency also tend to be represented by more codons, thus facilitating degeneracy in the code that might additionally facilitate functional variation in unknown ways. While it is now clear that natural selection acts on synonymous codons (10,11), the exact molecular traits upon ...
Bacteroides mobilizable and conjugative genetic elements
... mechanisms of horizontal gene transfer in prokaryotes, leading to genetic variation within a species and the acquisition of new traits, such as antibiotic resistance or the ability to produce toxins. Bacteroides conjugative transposons (CTn) were among the first transposons discovered, and they have ...
... mechanisms of horizontal gene transfer in prokaryotes, leading to genetic variation within a species and the acquisition of new traits, such as antibiotic resistance or the ability to produce toxins. Bacteroides conjugative transposons (CTn) were among the first transposons discovered, and they have ...
GENETIC ANALYSIS OF THE FUNCTION OF THE DROSOPHILA
... that this family of factors can form various combinations to alter downstream gene transcription. ...
... that this family of factors can form various combinations to alter downstream gene transcription. ...
Structural variations in the human genome
... in its broadest sense can even simply be defined as all genomic variations in an organisms genome that are bigger than one base pair (2). Several different types of mutations fit these two last definitions: deletions, insertions (novel sequence insertions and mobile-element insertions), inversions, ...
... in its broadest sense can even simply be defined as all genomic variations in an organisms genome that are bigger than one base pair (2). Several different types of mutations fit these two last definitions: deletions, insertions (novel sequence insertions and mobile-element insertions), inversions, ...
UV-Targeted Dinucleotides Are Not Depleted in Light
... et al. 2003; Rocap et al. 2003) and, therefore, exposed to different intensities of UV radiation. This seemed to make it an ideal model organism for investigating this hypothesis. Dufresne et al. (2003) have shown that the SS120 strain is adapted to living at a depth of 120 m. The MIT 9313 strain is ...
... et al. 2003; Rocap et al. 2003) and, therefore, exposed to different intensities of UV radiation. This seemed to make it an ideal model organism for investigating this hypothesis. Dufresne et al. (2003) have shown that the SS120 strain is adapted to living at a depth of 120 m. The MIT 9313 strain is ...
Sequence of the Tribolium castaneum Homeotic Complex
... clone (Falciani et al. 1996)] and the first candidate initiation methionine within the Tczen2 ORF. The proteins encoded by the Tribolium zen genes share regions of similar amino acids, one of which extends downstream of the homeodomain for several residues. The two Tribolium Zen proteins are more si ...
... clone (Falciani et al. 1996)] and the first candidate initiation methionine within the Tczen2 ORF. The proteins encoded by the Tribolium zen genes share regions of similar amino acids, one of which extends downstream of the homeodomain for several residues. The two Tribolium Zen proteins are more si ...
Nucleic Acids Research, 32: D489-D492 (2004).
... genome are Alu derived. All Alu-containing internal exons studied so far were found to be alternatively spliced (6). It was, thus, concluded that mutations resulting in constitutively spliced exonic Alus would result, in the vast majority of cases, in the creation of defective genes causing deleteri ...
... genome are Alu derived. All Alu-containing internal exons studied so far were found to be alternatively spliced (6). It was, thus, concluded that mutations resulting in constitutively spliced exonic Alus would result, in the vast majority of cases, in the creation of defective genes causing deleteri ...
in plant physiology
... multiple sigma factors in bryophytes may show a promoter preference and play roles in tissue-specific and stress-responsive transcriptional regulation in chloroplasts (Hara et al., 2001; Ichikawa et al., 2004; Kanazawa et al., 2013; Ueda, et al., 2013). Most NEP promoters (rpoB, rpoA, and accD) shar ...
... multiple sigma factors in bryophytes may show a promoter preference and play roles in tissue-specific and stress-responsive transcriptional regulation in chloroplasts (Hara et al., 2001; Ichikawa et al., 2004; Kanazawa et al., 2013; Ueda, et al., 2013). Most NEP promoters (rpoB, rpoA, and accD) shar ...
Phat—a gene finding program for Plasmodium falciparum
... zero, which we get around by adding a prior frequency count of one to all values. The probabilities for the reverse strand are also calculated from the observed frequency counts, with a few modifications. Appropriate adjustment also has to be made for the codon phase. If we define the first nucleoti ...
... zero, which we get around by adding a prior frequency count of one to all values. The probabilities for the reverse strand are also calculated from the observed frequency counts, with a few modifications. Appropriate adjustment also has to be made for the codon phase. If we define the first nucleoti ...
RNA Interference and Small Interfering RNAs
... transcribed, usually fully processed mRNA without an alteration in the rate of transcription of the target gene itself. If PTGS is explicitly mediated by dsRNA, the term RNA interference (RNAi) is preferred, but there may also be non-dsRNA sources, often termed aberrant RNAs, that may function as in ...
... transcribed, usually fully processed mRNA without an alteration in the rate of transcription of the target gene itself. If PTGS is explicitly mediated by dsRNA, the term RNA interference (RNAi) is preferred, but there may also be non-dsRNA sources, often termed aberrant RNAs, that may function as in ...
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.