Short tandem repeats (STRs), or microsatellites, are 1-6 base pair (bp) motifs of repeating units of DNA. (biomedcentral.com)
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)
Short tandem repeats (STRs) are widely present in the human genome. (researchsquare.com)
Short tandem repeats (STRs), also known as microsatellites, are repetitive DNA sequences consisting of 1-6-bp motifs present in a genome. (researchsquare.com)
Genome4
In other words, the direct repeats are nucleotide sequences present in multiple copies in the genome. (wikipedia.org)
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)
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)
Nucleotide sequences1
Nanopore sequencing is an evolving third/fourth generation sequencing technology for direct detection of nucleotide sequences with kb or even Mb base pairs (7)(8) . (researchsquare.com)
Putative1
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)
Mutations2
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)
Repetitive2
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)
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)
Loci1
These highly individual-specific number of repeats and the abundance of motifs have contributed to the polymorphism of STR loci. (researchsquare.com)
Developmental2
Such repeat expansions underlie several neurological and developmental disorders in humans. (wikipedia.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)
Genetic2
Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence. (wikipedia.org)
genetic analysis of cinnamyl alcohol dehydrogenase in loblolly pine: single gene inheritance, molecular characterization and evolution. (liverpool.ac.uk)
Present1
In the present study, genes across the 2q24-q33 interval were analyzed to identify an autism susceptibility gene in this region. (neurotransmitter.net)
Units1
The number of repeat units differs between individuals, resulting in highly complex allele polymorphisms. (researchsquare.com)
Transfer1
lipid transfer protein genes of loblolly pine are members of a complex gene family. (liverpool.ac.uk)
Long2
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)
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)
Expression2
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)
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)
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)
In other words, the direct repeats are nucleotide sequences present in multiple copies in the genome. (wikipedia.org)
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)
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)
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)
Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. (geneticsmr.com)
Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. (geneticsmr.com)
Amino acid sequences, exon-intron structure, motif details and subcellular localization pattern for all the 401 proteins are described. (bvsalud.org)
Pathogenic2
Moreover, these toxic, unexpected, homopolymeric proteins now should be considered in pathogenic models of microsatellite disorders. (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)
Polyglutamine2
Unexpectedly, we discovered that CAG expansion constructs express homopolymeric polyglutamine, polyalanine, and polyserine proteins in the absence of an ATG start codon. (nih.gov)
Additionally, we show that RAN translation across human spinocerebellar ataxia type 8 (SCA8) and myotonic dystrophy type 1 (DM1) CAG expansion transcripts results in the accumulation of SCA8 polyalanine and DM1 polyglutamine expansion proteins in previously established SCA8 and DM1 mouse models and human tissue. (nih.gov)
Amino1
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)
Cells2
This repeat-associated non-ATG translation (RAN translation) occurs across long, hairpin-forming repeats in transfected cells or when expansion constructs are integrated into the genome in lentiviral-transduced cells and brains. (nih.gov)
All above gene encoding transporters showed significant Cd transport activities using function assay in yeast cells. (bvsalud.org)
Proteins1
In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. (plos.org)
Genomes1
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)
Genomic1
Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. (ucsc.edu)
Markers4
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)
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)
The markers most commonly used are simple sequence repeat (SSR) or microsatellite markers. (geneticsmr.com)
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)
Occurs1
Generally, a direct repeat occurs when a sequence is repeated with the same pattern downstream. (wikipedia.org)
Sequence2
The nucleotide sequence written in bold characters signifies the repeated sequence. (wikipedia.org)
Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. (ucsc.edu)
Results2
These results have implications for understanding fundamental mechanisms of gene expression. (nih.gov)
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)
Analysis1
Using transcriptomic analysis, a total of 5238 differentially expressed genes were identified between the Cd treatment and control group. (bvsalud.org)
Level1
Increased ploidy level and individual repeats in high copy number are common in angiosperms but are rarely seen in gymnosperms [4] , [5] . (plos.org)
Regions1
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)