Origin and evolution of Y chromosomes: Drosophila tales
... sequencing and the development of proper bioinformatics methods enables a thorough molecular identification of the Y chromosome gene content [21–23]. Despite its large size (40 Mbp), it contains few single-copy protein-coding genes: 12 are currently known and indirect evidence suggests an upper bou ...
... sequencing and the development of proper bioinformatics methods enables a thorough molecular identification of the Y chromosome gene content [21–23]. Despite its large size (40 Mbp), it contains few single-copy protein-coding genes: 12 are currently known and indirect evidence suggests an upper bou ...
The dystrophin / utrophin homologues in Drosophila and in sea urchin
... non-muscle full length dystrophin isoforms transcribed from different promoters located in the 5 0 -end region of the gene, and four smaller proteins transcribed from internal promoters located further downstream, and lack important domains of dystrophin. Several other genes, encoding evolutionarily ...
... non-muscle full length dystrophin isoforms transcribed from different promoters located in the 5 0 -end region of the gene, and four smaller proteins transcribed from internal promoters located further downstream, and lack important domains of dystrophin. Several other genes, encoding evolutionarily ...
Playing by pair-rules?
... Thus far, similar patterns of wg and en have been found in all four of the major arthropod groups: hexapods (including insects),(reviewed in Ref. 4) crustaceans,(5–8) myriapods (millipedes and centipedes)(9) and chelicerates (spiders, mites, scorpions and horseshoe crabs)(10–12) (Fig. 1). In all cas ...
... Thus far, similar patterns of wg and en have been found in all four of the major arthropod groups: hexapods (including insects),(reviewed in Ref. 4) crustaceans,(5–8) myriapods (millipedes and centipedes)(9) and chelicerates (spiders, mites, scorpions and horseshoe crabs)(10–12) (Fig. 1). In all cas ...
POCUS: mining genomic sequence annotation to predict disease
... successful (0.8) and a more liberal value (0.5) for comparison. The results refer to the positive control sets of disease genes at the 0.8 threshold unless stated otherwise. POCUS was found to perform differently on the locus sets for different diseases. The method was successful (correctly identify ...
... successful (0.8) and a more liberal value (0.5) for comparison. The results refer to the positive control sets of disease genes at the 0.8 threshold unless stated otherwise. POCUS was found to perform differently on the locus sets for different diseases. The method was successful (correctly identify ...
Positive and Negative Selection on Noncoding
... in the genetic code (zero-fold-, 2-fold-, or 4-fold degenerate). We excluded potential splice sites of introns (defined as the first 6 bp or last 16 bp of an intron) from any analysis. We also categorized sites on the basis of their CpG-prone status (defined as being preceded by a C or followed by a ...
... in the genetic code (zero-fold-, 2-fold-, or 4-fold degenerate). We excluded potential splice sites of introns (defined as the first 6 bp or last 16 bp of an intron) from any analysis. We also categorized sites on the basis of their CpG-prone status (defined as being preceded by a C or followed by a ...
A conserved enhancer of the human and murine Hoxa
... Fig. 1. Constructs used to identify a minimal cis-acting upstream element specifying the anterior boundary of Hoxa-7 expression. (A) Genomic organisation of the Hoxa-7 locus spanning 7.1 kb. Boxes represent exons, hatched boxes indicate Hoxa-7 coding sequences, black boxes the homebox and stippled b ...
... Fig. 1. Constructs used to identify a minimal cis-acting upstream element specifying the anterior boundary of Hoxa-7 expression. (A) Genomic organisation of the Hoxa-7 locus spanning 7.1 kb. Boxes represent exons, hatched boxes indicate Hoxa-7 coding sequences, black boxes the homebox and stippled b ...
An accessible database for mouse and human whole transcriptome
... requires only basic sample preparation steps (reverse transcription of RNA). Double-stranded DNA dye (such as SYBR) based qPCR quantifies the amount of double-stranded DNA in a sample. A pair of specific primers amplifies a short (usually 60–130 bp) DNA region, and the emitted light is measured afte ...
... requires only basic sample preparation steps (reverse transcription of RNA). Double-stranded DNA dye (such as SYBR) based qPCR quantifies the amount of double-stranded DNA in a sample. A pair of specific primers amplifies a short (usually 60–130 bp) DNA region, and the emitted light is measured afte ...
A Complex Suite of Forces Drives Gene Traffic from Drosophila X
... genes from the X to the autosomes in both Drosophila melanogaster and humans (Betrán et al. 2002; Emerson et al. 2004; Potrzebowski et al. 2008). The autosomal copies of these paralogs tend to be testis expressed, suggesting that these new genes are preferentially retained because they allow for es ...
... genes from the X to the autosomes in both Drosophila melanogaster and humans (Betrán et al. 2002; Emerson et al. 2004; Potrzebowski et al. 2008). The autosomal copies of these paralogs tend to be testis expressed, suggesting that these new genes are preferentially retained because they allow for es ...
Evaluation of the phylogenetic position of the planctomycete
... They are supposed to have very strong resolving power in evaluating close and intermediate evolutionary distances, i.e. the relationships between species and between major lineages (Wolf et al., 2002). Besides concatenation of protein sequences, three different methods to infer phylogeny from coding ...
... They are supposed to have very strong resolving power in evaluating close and intermediate evolutionary distances, i.e. the relationships between species and between major lineages (Wolf et al., 2002). Besides concatenation of protein sequences, three different methods to infer phylogeny from coding ...
Genome organization of Magnaporthe grisea
... The filamentous ascomycetous fungus, Magnaporthe grisea (Hebert) Barr [(Pyricularia grisea, sacc) Pyricularia oryzae, cavara] is a causative agent of rice blast disease, one of the most devastating diseases of rice (Oryza sativa). Because of its economic importance, considerable efforts have been ma ...
... The filamentous ascomycetous fungus, Magnaporthe grisea (Hebert) Barr [(Pyricularia grisea, sacc) Pyricularia oryzae, cavara] is a causative agent of rice blast disease, one of the most devastating diseases of rice (Oryza sativa). Because of its economic importance, considerable efforts have been ma ...
Clustering of mandibular organ-inhibiting hormone and moult
... MIH genes clustered within 6.5 kb. The other type contains only the MO-IH-2 gene, which is not closely linked to an MIH gene. There are three exons and two introns in all MIH and MO-IH genes analysed. The exon–intron boundary of the crab MIH and MO-IH genes follows Chambon’s rule (GT–AG) for the spl ...
... MIH genes clustered within 6.5 kb. The other type contains only the MO-IH-2 gene, which is not closely linked to an MIH gene. There are three exons and two introns in all MIH and MO-IH genes analysed. The exon–intron boundary of the crab MIH and MO-IH genes follows Chambon’s rule (GT–AG) for the spl ...
Application of rpoB sequence similarity analysis, REP‐PCR and
... 2004). Therefore, studying phylogenetic relations and diversity in this novel bacterial genus is not only a taxonomical concern, but also a necessity in order to exploit its biotechnological potential completely. ...
... 2004). Therefore, studying phylogenetic relations and diversity in this novel bacterial genus is not only a taxonomical concern, but also a necessity in order to exploit its biotechnological potential completely. ...
Biomart/ GENOME ALIGNMENT III
... under selection are enhanced with the addition of more sequences and this observation has led to numerous ‘focused sequencing’ projects which seek to obtain sequence for a small region of a genome in numerous other organisms. Biologists who seek to analyze conserved regions among homologous sequence ...
... under selection are enhanced with the addition of more sequences and this observation has led to numerous ‘focused sequencing’ projects which seek to obtain sequence for a small region of a genome in numerous other organisms. Biologists who seek to analyze conserved regions among homologous sequence ...
Sequence Alignment - Bilkent University
... mutation of pre-existing intronic sequences that result in the recruitment of intronic sequences into coding regions of mRNAs. This process is called exonization. ...
... mutation of pre-existing intronic sequences that result in the recruitment of intronic sequences into coding regions of mRNAs. This process is called exonization. ...
Gene Nomenclature System for Rice
... The current rules for gene names and gene symbols in rice are based on recommendations from the Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative [12]. Most of the early gene names and symbols are descriptive of visible phenotypes that provided the ea ...
... The current rules for gene names and gene symbols in rice are based on recommendations from the Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative [12]. Most of the early gene names and symbols are descriptive of visible phenotypes that provided the ea ...
A natural chimeric yeast containing genetic material from three species
... Saccharomyces bayanus-like, are ubiquitous and contributed parts of the nuclear genome ; the third, Saccharomyces sp. IFO 1802-like, which has been found only in Japan, contributed the mitochondrial DNA molecule. These data suggest that the yeast cell is able to accommodate, express and propagate ge ...
... Saccharomyces bayanus-like, are ubiquitous and contributed parts of the nuclear genome ; the third, Saccharomyces sp. IFO 1802-like, which has been found only in Japan, contributed the mitochondrial DNA molecule. These data suggest that the yeast cell is able to accommodate, express and propagate ge ...
Distinct functions of two olfactory marker protein genes derived from
... vertebrate evolution. Two rounds of WGD (1R and 2R) occurred in the common ancestor of Gnathostomata and Cyclostomata, followed by the third-round WGD (3R) in a common ancestor of all modern teleosts. The 3R-derived paralogs are good models for understanding the evolution of genes after WGD, which h ...
... vertebrate evolution. Two rounds of WGD (1R and 2R) occurred in the common ancestor of Gnathostomata and Cyclostomata, followed by the third-round WGD (3R) in a common ancestor of all modern teleosts. The 3R-derived paralogs are good models for understanding the evolution of genes after WGD, which h ...
Gene Duplication - Semantic Scholar
... the duplication of a segment of DNA that has 1,000 nucleotides or more. In addition to unequal crossing-over, segmental duplication can also arise via some other mechanisms that are not well understood. See Marques-Bonet, et al. 2009 for a recent review on ...
... the duplication of a segment of DNA that has 1,000 nucleotides or more. In addition to unequal crossing-over, segmental duplication can also arise via some other mechanisms that are not well understood. See Marques-Bonet, et al. 2009 for a recent review on ...
Evolution of a pseudo-control region in the mitochondrial genome of
... approach a 2.5 kb PCR fragment comprising the section between ND6 and 12s genes was isolated from Buteo buteo hureo,cloned and sequenced. The gene order corresponds to the novel arrangement described for Folco peregrinrrs by Mindell et al. (1998). The fragment includes a non coding section between t ...
... approach a 2.5 kb PCR fragment comprising the section between ND6 and 12s genes was isolated from Buteo buteo hureo,cloned and sequenced. The gene order corresponds to the novel arrangement described for Folco peregrinrrs by Mindell et al. (1998). The fragment includes a non coding section between t ...
A program for annotating and predicting the effects of single
... Our previous analyses suggest that most of the SNPs that we identified in w1118 ; iso-2; iso-3 are probably genuine and can be validated by capillary sequencing.1 A common worry about nextgeneration sequencing data in general is that SNPs are vastly over estimated. One might thing that if a large fr ...
... Our previous analyses suggest that most of the SNPs that we identified in w1118 ; iso-2; iso-3 are probably genuine and can be validated by capillary sequencing.1 A common worry about nextgeneration sequencing data in general is that SNPs are vastly over estimated. One might thing that if a large fr ...
Gene Regulatory Network of Ikaros in T cell development and
... risks of relapse of leukemia and poor outcome of therapy. However, it remains unclear about the gene regulatory network associated with Ikaros. How exactly the transcription of Ikaros itself is regulated? Ikaros can positively or negatively regulate its target genes, and how Ikaros' activity is regu ...
... risks of relapse of leukemia and poor outcome of therapy. However, it remains unclear about the gene regulatory network associated with Ikaros. How exactly the transcription of Ikaros itself is regulated? Ikaros can positively or negatively regulate its target genes, and how Ikaros' activity is regu ...
A large scale analysis of resistance gene
... A. thaliana for resistance to Pseudomonas syringae (gi 15221252), R-gene Mi-1 against nematodes and aphids from Lycopersicon esculentum (gi 7489037) and gene Rpp 8 of A. thaliana (gi 17064876). The sequence of primer RNBS-D-rev was kindly provided by Nevin Young. Primer LM638 was developed by Kanazi ...
... A. thaliana for resistance to Pseudomonas syringae (gi 15221252), R-gene Mi-1 against nematodes and aphids from Lycopersicon esculentum (gi 7489037) and gene Rpp 8 of A. thaliana (gi 17064876). The sequence of primer RNBS-D-rev was kindly provided by Nevin Young. Primer LM638 was developed by Kanazi ...
Mapping the genes that made maize
... teosinte ears. They suggested that each of the four chromosomal segments contained a group of morphological genes rather than a single gene, although they presented no evidence to support this view. Mangelsdorf5 reported that these four segments probably map to chromosomes 1, 3, 4 and 9, but again:h ...
... teosinte ears. They suggested that each of the four chromosomal segments contained a group of morphological genes rather than a single gene, although they presented no evidence to support this view. Mangelsdorf5 reported that these four segments probably map to chromosomes 1, 3, 4 and 9, but again:h ...
Occurrence of phosphate acquisition genes in Prochlorococcus cells
... From the analysis of P acquisition genes in Prochlorococcus strains, it was clear that the presence or absence of these genes did not correspond with major phylogenetic groupings (Martiny et al., 2006). However, the distribution of phosphate acquisition genes in Prochlorococcus could still be explai ...
... From the analysis of P acquisition genes in Prochlorococcus strains, it was clear that the presence or absence of these genes did not correspond with major phylogenetic groupings (Martiny et al., 2006). However, the distribution of phosphate acquisition genes in Prochlorococcus could still be explai ...
Comparison of Statistical Models for Affymetrix GeneChip
... this does not necessarily mean that the mismatch probes are a good idea - but if they are present we should use them we have demonstrated this using both analytic considerations and experimental data a carefully designed experiment can be used to address many issues Many more genes may be expressed ...
... this does not necessarily mean that the mismatch probes are a good idea - but if they are present we should use them we have demonstrated this using both analytic considerations and experimental data a carefully designed experiment can be used to address many issues Many more genes may be expressed ...
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.