Eukaryotic genomesWhole-genomeMutationsEvolutionarySequencesVariantsRepetitiveLocusMutationDetectMolecularGeneticShortFoundImportant roleDiseaseStudyCoding and non-codingSingleVarietyLengthPresenceSequenceChloroplast genomeComplete chloroplastPhylogeneticHomologyTractsMRNASpeciesAnnotationAnalysesAminoGenomicProteinsAngiospermsStructureAnalysisAdditionReferenceContentFunctionsSignificantRegionsResultsExtensiveRegionTotalTime
Eukaryotic genomes1
- they found out that more than half of the eukaryotic genomes were repetitive DNA through their experiments on reassociation of DNA. (wikipedia.org)
Whole-genome2
- To estimate the genome-wide pattern of mutations at STR loci, we analyze blood-derived whole-genome sequencing data for 544 individuals from 29 three-generation CEPH pedigrees. (biomedcentral.com)
- human whole-genome. (scirp.org)
Mutations6
- Short tandem repeats (STRs) compose approximately 3% of the genome, and mutations at STR loci have been linked to dozens of human diseases including amyotrophic lateral sclerosis, Friedreich ataxia, Huntington disease, and fragile X syndrome. (biomedcentral.com)
- Improving our understanding of these mutations would increase our knowledge of the mutational dynamics of the genome and may uncover additional loci that contribute to disease. (biomedcentral.com)
- Approximately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but only 10% are found in LINE-1 insertions, which compose 17% of the genome. (biomedcentral.com)
- We estimate the average number of de novo genome-wide STR mutations per individual to be approximately 85, which is similar to the average number of observed de novo single nucleotide variants. (biomedcentral.com)
- We hypothesize that there might be at least three types of autism susceptibility genes/mutations that can be (i) specific to an individual patient or family, (ii) in a genetically isolated sub-population and (iii) a common factor shared amongst different populations. (neurotransmitter.net)
- The genes/mutations could act alone or interact with other genetic and/or epigenetic or environmental factors, causing autism or related disorders. (neurotransmitter.net)
Evolutionary1
- In the 1990s, more research was conducted to elucidate the evolutionary dynamics of minisatellite and microsatellite repeats because of their importance in DNA-based forensics and molecular ecology. (wikipedia.org)
Sequences8
- Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. (wikipedia.org)
- Some of these repeated sequences are necessary for maintaining important genome structures such as telomeres or centromeres. (wikipedia.org)
- Repeated sequences are categorized into different classes depending on features such as structure, length, location, origin, and mode of multiplication. (wikipedia.org)
- While some repeated DNA sequences are important for cellular functioning and genome maintenance, other repetitive sequences can be harmful. (wikipedia.org)
- Overall, repeated sequences are an important area of focus because they can provide insight into human diseases and genome evolution. (wikipedia.org)
- McClintock's work set the stage for the discovery of repeated sequences because transposition, centromere structure, and telomere structure are all possible through repetitive elements, yet this was not fully understood at the time. (wikipedia.org)
- Many repeat sequences are likely to be non-functional, decaying remnants of Transposable elements, these have been labelled "junk" or "selfish" DNA. (wikipedia.org)
- Tandem repeats are repeated sequences which are directly adjacent to each other in the genome. (wikipedia.org)
Variants1
- The first stage involved identifying, in unrelated subjects showing linkage to 2q24-q33, genetic variants in exons and flanking sequence within candidate genes and comparing the frequency of the variants between autistic and unrelated nonautistic subjects. (neurotransmitter.net)
Repetitive2
- The disposition of repetitive elements throughout the genome can consist either in directly adjacent arrays called tandem repeats or in repeats dispersed throughout the genome called interspersed repeats. (wikipedia.org)
- In the 2000s, the data from full eukaryotic genome sequencing enabled the identification of different promoters, enhancers, and regulatory RNAs which are all coded by repetitive regions. (wikipedia.org)
Locus1
- For minisatellites and microsatellites, the number of times the sequence repeats at a single locus can range from twice to hundreds of times. (wikipedia.org)
Mutation2
- from the mutation of a single gene. (scirp.org)
- METHOD: Mutation screening of positional candidate genes was performed in two stages. (neurotransmitter.net)
Detect1
- Some of these tools are designed to detect STR expansions at disease-related loci, while others detect expansions and contractions of STRs genome-wide but are constrained by sequencing read length and the STR motif size. (biomedcentral.com)
Molecular1
- To address the molecular and cellular events that lead to these pathological outcomes, we recently generated a mouse Dmpk CTG expansion knock-in model and identified choroid plexus epithelial cells as particularly affected by the expression of toxic CUG expansion RNAs. (bvsalud.org)
Genetic1
- DNA-dispersed repeats were increasingly recognized as a potential source of genetic variation and regulation. (wikipedia.org)
Short2
- When the repeating sequence is only 2-10 nucleotides long, the repeat is referred to as a short tandem repeat (STR) or microsatellite. (wikipedia.org)
- Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
Found1
- Negative association findings and research involving the serotonin transporter gene, FMR1, RELN, WNT2, HOXA1, and HOXB1 genes may be found elsewhere on this site . (neurotransmitter.net)
Important role1
- In addition to playing an important role in recombination, tandem repeats also play important structural roles in the genome. (wikipedia.org)
Disease2
- ease or are within disease genes. (scirp.org)
- Myotonic dystrophy type 1 is a dominantly inherited multisystemic disease caused by CTG tandem repeat expansions in the DMPK 3' untranslated region. (bvsalud.org)
Study1
- In the present study, genes across the 2q24-q33 interval were analyzed to identify an autism susceptibility gene in this region. (neurotransmitter.net)
Coding and non-coding1
- STRs are distributed throughout the genome and are located in both coding and non-coding regions [ 2 ]. (biomedcentral.com)
Single1
- Two single nucleotide polymorphisms (SNPs) that showed evidence for divergent distribution between autistic and nonautistic subjects were identified, both within SLC25A12, a gene encoding the mitochondrial aspartate/glutamate carrier (AGC1). (neurotransmitter.net)
Variety1
- Tandem repeats have a wide variety of biological functions in the genome. (wikipedia.org)
Length1
- Tandem repeats and interspersed repeats are further categorized into subclasses based on the length of the repeated sequence and/or the mode of multiplication. (wikipedia.org)
Presence1
- The presence of repeated sequence DNA makes it easier for areas of homology to align, thereby controlling when and where recombination occurs. (wikipedia.org)
Sequence15
- Tandem repeats and interspersed repeats are further categorized into subclasses based on the length of the repeated sequence and/or the mode of multiplication. (wikipedia.org)
- Tandem repeats may vary in the number of nucleotides comprising the repeated sequence, as well as the number of times the sequence repeats. (wikipedia.org)
- When the repeating sequence is only 2-10 nucleotides long, the repeat is referred to as a short tandem repeat (STR) or microsatellite. (wikipedia.org)
- When the repeating sequence is 10-60 nucleotides long, the repeat is referred to as a minisatellite. (wikipedia.org)
- For minisatellites and microsatellites, the number of times the sequence repeats at a single locus can range from twice to hundreds of times. (wikipedia.org)
- The presence of repeated sequence DNA makes it easier for areas of homology to align, thereby controlling when and where recombination occurs. (wikipedia.org)
- In this study, we searched the human genome reference sequence and annotated exons (exome) for the presence of uninterrupted triplet repeat tracts composed of six or more repeated units. (nih.gov)
- Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. (ucsc.edu)
- Objectives: Present study was conducted to study and compare the complete chloroplast sequence of G. thurberi, analyses of its genome structure, gene content and organization, repeat sequence and codon usage and comparison with two cultivated allotetraploid sequenced cotton species. (ijbiotech.com)
- To determine the repeat sequence and location, an online version of REPuter was used. (ijbiotech.com)
- Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. (biomedcentral.com)
- Comparative genome analysis showed low sequence variability. (biomedcentral.com)
- Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. (plos.org)
- Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. (plos.org)
- A whole genome sequence comparison of AK164 with type strains from the same genus, using digital DNA-DNA hybridization and average nucleotide identity calculations, revealed that AK164 might potentially belong to a new species of Isoptericola. (bvsalud.org)
Chloroplast genome6
- Therefore and In addition to phylogenetic analysis based on plastidic genomes, it is imperative to understand the chloroplast genome in order to logically design our next generation transplastomics. (ijbiotech.com)
- G. barbadense and G. hirsutum are extensively cultivated in the world and their chloroplast genome sequences have been published. (ijbiotech.com)
- Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. (biomedcentral.com)
- The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. (biomedcentral.com)
- Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. (biomedcentral.com)
- And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. (biomedcentral.com)
Complete chloroplast1
- The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. (biomedcentral.com)
Phylogenetic1
- Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma , Sycomorus , and Ficus , respectively. (biomedcentral.com)
Homology1
- A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. (plos.org)
Tracts1
- Surprisingly, many groups of genes that contain TNR types coding for different homo-amino acid tracts associate with the same transcription-related GO categories. (nih.gov)
MRNA1
Species2
- Few differences have been reported in the same species, but significant differences could be detected between the different species in genome size and gene orientation (5). (ijbiotech.com)
- Gossypium includes 52 species that are divided to eight diploid genome A-G and K (2n=26), and one allotetraploid genome (AADD, 2n=52). (ijbiotech.com)
Annotation1
- Gene annotation was mainly performed by DOGMA. (ijbiotech.com)
Analyses1
- Genome data and biochemical analyses indicate that AK164 could be a potential biostimulant for improving agriculture in submerged saline land. (bvsalud.org)
Amino1
- Other expanded repeats can be translated into proteins containing a pathogenic stretch of repeated amino acids by a novel mechanism called repeat-associated non-AUG (RAN) translation [ 12 ], and these proteins could contain compositionally biased amino acids. (biomedcentral.com)
Genomic2
- Despite the high level of conservation in cp genome SSRs ,these are useful in analysis of genetic diversity due to their greater efficiency as opposed to genomic SSRs. (ijbiotech.com)
- These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution. (plos.org)
Proteins2
Angiosperms3
- Gymnosperms have undergone 300 million years of evolution since their divergence from the ancestors of modern angiosperms, and they possess enormously complex genomes in comparison [1] - [3] . (plos.org)
- Increased ploidy level and individual repeats in high copy number are common in angiosperms but are rarely seen in gymnosperms [4] , [5] . (plos.org)
- While rapid progress has been made in characterizing the genomes of angiosperms, the same is not true for gymnosperms, in part due to an order of magnitude increase in their size and complexity. (plos.org)
Structure3
- The map of genome structure and gene distribution were carried out using OGDRAW V1.1. (ijbiotech.com)
- Results: The G. thurberi chloroplast (cp) genome is 160264 bp in length with conserved quadripartite structure. (ijbiotech.com)
- Chloroplasts have low mutation rate with great deal of conservation in their genome size and structure, gene content and organization. (ijbiotech.com)
Analysis1
- Using transcriptomic analysis, a total of 5238 differentially expressed genes were identified between the Cd treatment and control group. (bvsalud.org)
Addition2
- In addition to playing an important role in recombination, tandem repeats also play important structural roles in the genome. (wikipedia.org)
- In addition, these CP genomes showed variation in their inverted repeat regions (IR). (biomedcentral.com)
Reference1
- Recent advances in the cost and utility of second generation, high-throughput sequencing technologies have made it possible for ten conifer reference genomes to be assembled ( http://www.pinegenome.org/pinerefseq ). (plos.org)
Content1
- Low GC content is a significant feature of plastidic genomes, which is possibly formed after endosymbiosis by DNA replication and repair. (ijbiotech.com)
Functions3
- Nevertheless, occasionally some repeats may be exapted for other functions. (wikipedia.org)
- Tandem repeats have a wide variety of biological functions in the genome. (wikipedia.org)
- Most genes containing exon-overrepresented TNRs are associated with gene ontology-defined functions. (nih.gov)
Significant1
- All above gene encoding transporters showed significant Cd transport activities using function assay in yeast cells. (bvsalud.org)
Regions4
- CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. (ucsc.edu)
- The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. (ucsc.edu)
- Single copy region of cp genome is separated by the two inverted regions. (ijbiotech.com)
- Most plastidic genomes have four regions, namely large single copy region (LSC, 80 Kb), small single copy region (SSC, 20 kb) and two inverted repeat regions (IR, 25 kb). (ijbiotech.com)
Results1
- This is the first study on the MATE genes in mangroves and the results provide comprehensive information on the molecular mechanisms enabling the survival of mangroves under hostile conditions. (bvsalud.org)
Extensive1
- The custom designed repeat masking libraries generated for each of these genomes, which will be of extensive use for the researchers worldwide, are also provided in this paper. (bvsalud.org)
Region1
- The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. (ucsc.edu)
Total1
- A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. (biomedcentral.com)
Time2
- MATE transporters, which play crucial roles in the survival of mangrove plants under highly challenged environments, by specialized salt extrusion mechanisms, are mined from their genomes and reported here for the first time. (bvsalud.org)
- To evaluate the origin and time since spreading of the 999del5 mutation in Iceland and in Finland, we constructed haplotypes with polymorphic markers within and flanking the BRCA2 gene in a set of 18 Icelandic and 10 Finnish 999del5 breast cancer families. (nih.gov)