• There are several types of repeated sequences : Interspersed (or dispersed) DNA repeats (interspersed repetitive sequences) are copies of transposable elements interspersed throughout the genome. (wikipedia.org)
  • citation needed] The ribosomal RNA and transfer RNA genes belong to the class of middle repetitive DNA. (wikipedia.org)
  • A tract of repetitive DNA in which a motif of a few base pairs is tandemly repeated numerous times (e.g. 5 to 50 times) is referred to as microsatellite DNA. (wikipedia.org)
  • in contrast to simple family structures reported for a variety of angiosperm nsltp genes, the putative pine nsltp gene is a member of a complex family. (liverpool.ac.uk)
  • In other words, the direct repeats are nucleotide sequences present in multiple copies in the genome. (wikipedia.org)
  • The nucleotide sequence written in bold characters signifies the repeated sequence. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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 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)
  • These highly individual-specific number of repeats and the abundance of motifs have contributed to the polymorphism of STR loci. (researchsquare.com)
  • Flanking (or terminal) repeats (terminal repeat sequences) are sequences that are repeated on both ends of a sequence, for example, the long terminal repeats (LTRs) on retroviruses. (wikipedia.org)
  • Tandem repeats (tandem repeat sequences) are repeated copies which lie adjacent to each other. (wikipedia.org)
  • Thus direct repeat tandem sequences are a form of microsattelite DNA. (wikipedia.org)
  • In directly repeated sequences of the tobacco plant genome, DNA double-strand breaks can be efficiently repaired by homologous recombination between the repeated sequences. (wikipedia.org)
  • Siebert R, Puchta H. Efficient repair of genomic double-strand breaks by homologous recombination between directly repeated sequences in the plant genome. (wikipedia.org)
  • 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)
  • Such repeat expansions underlie several neurological and developmental disorders in humans. (wikipedia.org)
  • These expanded repeats are transcribed and produce toxic CUG RNAs that sequester and inhibit activities of the MBNL family of developmental RNA processing factors. (bvsalud.org)
  • the gene encoding the monolignol biosynthetic enzyme cinnamyl alcohol dehydrogenase (cad, e.c. 1.1.1.195) can be expressed in response to different developmental and environmental cues. (liverpool.ac.uk)
  • 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)
  • genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution. (liverpool.ac.uk)
  • Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence. (wikipedia.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)
  • In the present study, genes across the 2q24-q33 interval were analyzed to identify an autism susceptibility gene in this region. (neurotransmitter.net)
  • The number of repeat units differs between individuals, resulting in highly complex allele polymorphisms. (researchsquare.com)
  • 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)
  • control of cad gene expression could involve either differential regulation of more than one cad gene or, alternatively combinatorial regulation of a single cad gene. (liverpool.ac.uk)
  • xylem-specific gene expression in loblolly pine. (liverpool.ac.uk)
  • NanoSTR can be used for STR detection and genotyping based on long-read data from nanopore sequencing with improved accuracy and efficiency compared with other existing methods, such as Tandem-Genotypes and TRiCoLOR. (researchsquare.com)
  • Tandem-Genotypes requires data preprocessing steps such as LAST alignment and establishment of a genomic background database, and histograms are needed to assist STR genotyping. (researchsquare.com)
  • lipid transfer protein genes of loblolly pine are members of a complex gene family. (liverpool.ac.uk)
  • Generally, a direct repeat occurs when a sequence is repeated with the same pattern downstream. (wikipedia.org)
  • Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence. (wikipedia.org)
  • Generally, a direct repeat occurs when a sequence is repeated with the same pattern downstream. (wikipedia.org)
  • The nucleotide sequence written in bold characters signifies the repeated sequence. (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)
  • 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)
  • 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)
  • In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. (geneticsmr.com)
  • The markers most commonly used are simple sequence repeat (SSR) or microsatellite markers. (geneticsmr.com)
  • Whole genome sequence and expressed sequence tags (ESTs) of the eucalypts paved way for introduction of molecular genetics and breeding in this genus. (springeropen.com)
  • Different molecular characterization approaches have been used simultaneously in eucalypts, however, microsatellites or simple sequence repeats (SSRs) with their prolific characteristics could occupy a special niche in Eucalyptus genetic improvement. (springeropen.com)
  • One of the most frequently used DNA markers in eucalypts since 1996 are microsatellites or simple sequence repeats (SSRs) (Byrne et al. (springeropen.com)
  • Subsequently, development of online databases like GenBank led to the generation of Expressed Sequence Tag (EST) derived-SSRs (eSSRs) which are present in transcribed regions of the genome. (springeropen.com)
  • 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)
  • We show that mutagenesis of the N-terminal KRIT1 NPXY amino acid sequence, a motif critical for ICAP-1 binding to beta1 integrin molecules, completely abrogates the KRIT1/ICAP-1 interaction. (nih.gov)
  • These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution. (plos.org)
  • This review on eucalypts microsatellites, highlights the availability and characteristics of genomic and eSSRs and their potential in genetic analysis of natural and breeding populations and also discusses the future prospects in population genetics and marker assisted selection. (springeropen.com)
  • 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)
  • 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)
  • A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. (plos.org)
  • mrna Chimp mRNAs Chimp mRNAs from GenBank mRNA and EST Description The mRNA track shows alignments between chimp mRNAs in GenBank and the genome. (ucsc.edu)
  • Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus . (geneticsmr.com)
  • citation needed] The ribosomal RNA and transfer RNA genes belong to the class of middle repetitive DNA. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • Their particular strength lies in the fact that they are spread throughout the genome, do not require large amounts of DNA for analysis, are reliable and generate multiple markers, and their use does not require any prior genome information. (geneticsmr.com)
  • The importance of microsatellites for plant genome analysis has been highlighted on several occasions (Varshney et al. (springeropen.com)
  • Using transcriptomic analysis, a total of 5238 differentially expressed genes were identified between the Cd treatment and control group. (bvsalud.org)
  • 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)
  • 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)
  • 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)
  • Increased ploidy level and individual repeats in high copy number are common in angiosperms but are rarely seen in gymnosperms [4] , [5] . (plos.org)
  • 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)
  • All above gene encoding transporters showed significant Cd transport activities using function assay in yeast cells. (bvsalud.org)