Nucleotide base. Medical search. Frequent questions

Aligning the single nucleotide polymorphisms (SNPs) from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. (nih.gov)
plural SNPs /snɪps/) is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population (generally regarded as 1% or more). (wikipedia.org)
Variant" may also be used as a general term for any single nucleotide change in a DNA sequence, encompassing both common SNPs and rare mutations, whether germline or somatic. (wikipedia.org)
While CNVs usually cover large DNA sequence variations, single nucleotide polymorphisms or SNPs are random, single base substitutions found throughout the genome. (jove.com)
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaptation that optimizes population survival in differing environments. (scirp.org)
Variations in toxicity and response to therapy are observed among patients despite similar clinicopathologic characteristics which are attributed to single nucleotide polymorphisms (SNPs). (researchsquare.com)
So, the aim of this review was to investigate the effect of single nucleotide polymorphisms (SNPs) on response rate and toxicity in HNSCCs. (researchsquare.com)
We compared two methods to model the combined effect of 14 prostate cancer risk-associated SNPs and family history for the estimation of absolute risk for prostate cancer in a population-based case-control study in Sweden (2,899 cases and 1,722 controls). (johnshopkins.edu)
The aim of this study was to identify any impact of CYP2A13 single-nucleotide polymorphisms (SNPs) on CYP2A13 expression in human lung. (aspetjournals.org)
To date, more than 20 single-nucleotide polymorphisms (SNPs) have been identified in CYP2A13 (Zhang et al. (aspetjournals.org)

Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions(regions between genes). (wikipedia.org)
As a sub-objective, since PDE10A transcript variants were reported strictly through analyses of bovine genomic sequence, we also wanted to determine the nucleotide and amino acid sequences by experimental evidence. (plos.org)
Promoter region sequences were extracted oil palm genome spanning from 1500 nucleotides (nt) upstream to 1000 nt downstream of every annotated transcription start sites (TSS). (bvsalud.org)
Homologous recombination involves the exchange of nucleotide sequences to repair damaged bases on both strands of DNA through the utilization of a sister chromatid. (news-medical.net)
The new features allow users to 1) add primer annotations or other data sets in batch mode, 2) export differences between sequences to other genome browsers, 3) compare multiple genomes at a single nucleotide level of detail, 4) create new alignments from subsets/subsequences of a very large master alignment and 5) allow display of summaries of deep RNA sequencing data sets on a genome sequence. (biomedcentral.com)
Key distinctive features of the original BBB were its ability to read annotations (CDS positions) from GenBank files, an explicit display of differences between sequences and a tool to compare genomes, including the ability to summarize the consequences of all nucleotide changes on encoded proteins throughout a genome. (biomedcentral.com)
Phylogenetic tree constructed by the neighbor-joining method based on the partial sequences of HEV ORF1 gene. (scielo.br)
The nucleotide sequences found in the present study (9B and A1) are narrowed with diamonds. (scielo.br)
This technology involves breaking the entire genome into small segments, sequencing the segments, and then reassembling the sequences using intensive computational techniques to provide the base-by-base sequence of the entire genome or more limited regions, such as the expressed portion of the genome known as the exome. (msdmanuals.com)

For example, a G nucleotide present at a specific location in a reference genome may be replaced by an A in a minority of individuals. (wikipedia.org)
We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. (nature.com)
Single-stranded annealing provides end joining between interspersed nucleotide repeats within the genome leading to one copy of the repeat and the intervening sequence being deleted in the process. (news-medical.net)
Disease risk-associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies have the potential to be used for disease risk prediction. (johnshopkins.edu)
We used the bivariate causal mixture model (MiXeR) to quantify genome-wide polygenic overlap and the conditional/conjunctional false discovery rate (pleioFDR) method to identify shared loci, based on genome-wide association study summary statistics on depression (n = 450,619), coronary artery disease (n = 502,713) and nine cardiovascular risk factors (n = 204,402-776,078). (plos.org)

Single nucleotide substitutions with an allele frequency of less than 1% are sometimes called single-nucleotide variants (SNVs). (wikipedia.org)
Except for lacking exons, these pseudogenes contained several nucleotide substitutions, insertions and deletions. (yourdictionary.com)
Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. (lu.se)

Goupil S, Maréchal L, El Hajj H, Tremblay M-È, Richard FJ, Leclerc P (2016) Identification and Localization of the Cyclic Nucleotide Phosphodiesterase 10A in Bovine Testis and Mature Spermatozoa. (plos.org)

Senior author Lukas Dow , PhD, an Associate Professor of Biochemistry In Medicine at Weill Cornell Medicine, and his colleagues genetically engineered mice to carry an enzyme that allows the scientists to change a single base or "letter" in the mouse's genetic code. (bioquicknews.com)
We demonstrate that TdT-dNTP conjugates can quantitatively extend a primer by a single nucleotide in 10-20 s, and that the scheme can be iterated to write a defined sequence. (nature.com)
Figure 2: TdT-dNTP conjugates can extend a DNA molecule by a single nucleotide in 10-20 s, enabling stepwise DNA synthesis. (nature.com)
A single nucleotide polymorphism (abbreviated SNP, pronounced snip) is a genomic variant at a single base position in the DNA. (genome.gov)
Single nucleotide polymorphism, or SNP. (genome.gov)
With the development of high throughput technologies such as tandem mass spectrometry (MS/MS) and next generation sequencing, more and more nonsynonymous single-nucleotide variations (nsSNVs) that cause variation of amino acids have been identified, some of which result in the damage of PTMs. (hindawi.com)
Either at genomic or at proteomic level, mutations have significant impact on normal gene or protein function, and human diseases could be associated with mutations like nonsynonymous single-nucleotide variations (nsSNVs) on amino acids. (hindawi.com)
Genomic variations in a population can arise due to single nucleotide changes in the DNA or structural changes to chromosomes. (jove.com)
For example, in patients with sickle cell anemia, a single base substitution from adenine to thymine in a specific locus of the beta-globin gene causes sickle-shaped red blood cells. (jove.com)
These variations can be a single nucleotide or a larger chromosomal variation. (jove.com)
The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1% of the population. (jove.com)
Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. (frontiersin.org)
Identification of oil palm cis-regulatory elements based on DNA free energy and single nucleotide polymorphism density. (bvsalud.org)
using the combination of DNA free energy and single nucleotide polymorphism (SNP) density approaches. (bvsalud.org)
A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. (animbiosci.org)
Base-excision repair involves the recognition and removal of a single damaged base. (news-medical.net)
It also discovered a single letter change in the genetic code, single nucleotide polymorphism (SNP). (yourdictionary.com)
NextGene analysis provided higher sensitivity, as four previously undetected single-nucleotide variations were found. (nih.gov)
Analysis of radioactive and nonradioactive purine bases, purine nucleosides and purine nucleotides by high-speed chromatography on a single column. (elsevierpure.com)
indicates amino acid change that require more complex mutation than single nucleotide substitution. (lu.se)
indicates codon change that single nucleotide doesn't change amino acid (silent mutation). (lu.se)
This process helps identify single or multiple nucleotide variations as well as areas of insertion or deletion. (msdmanuals.com)
Multiple distinct single- and double-nucleotide substitution signatures were discernible. (lu.se)

Adenine and guanine are purine bases. (knowgenetics.org)
It is known to act through protein phosphorylation via PRKA and through the activation of guanine nucleotide exchange factors like EPAC. (plos.org)
Methylation of guanine bases produces a change in the structure of DNA by forming a product that is complimentary to thymine rather than cytosine. (news-medical.net)
The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. (medlineplus.gov)

The first three have apparently evolved from the adenine nucleotide carrier. (yourdictionary.com)

The two possible nucleotide variations of this SNP - G or A - are called alleles. (wikipedia.org)
Copy number variation or CNV is an umbrella term that defines the structural variations involving DNA segments of more than 1 kilo base pair. (jove.com)

It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. (yourdictionary.com)
The full-length sequence exhibits little overall homology to any other known protein at either the nucleotide or the amino acid level. (yourdictionary.com)

The sugar and phosphate group make up the backbone of the DNA double helix, while the bases are located in the middle. (knowgenetics.org)
A chemical bond between the phosphate group of one nucleotide and the sugar of a neighboring nucleotide holds the backbone together. (knowgenetics.org)

Chemical bonds (hydrogen bonds) between the bases that are across from one another hold the two strands of the double helix together. (knowgenetics.org)
Nucleotides are arranged in two long strands that form a spiral called a double helix. (medlineplus.gov)

We find useful ranges of properties for DNA polymerase-based recorders, providing guidance for future protein engineering attempts. (mit.edu)
The enzymes remove the damaged base forming an AP site which is repaired by AP endonuclease before the nucleotide gap in the DNA strand is filled by DNA polymerase. (news-medical.net)
The third excision mechanism is called mismatch repair and occurs when mismatched bases are incorporated into the DNA strand during replication and are not removed by proofreading DNA polymerase. (news-medical.net)

The non-defective strand is used as a template with the damaged DNA on the other strand removed and replaced by the synthesis of new nucleotides. (news-medical.net)

Both cidofovir and adefovir are nucleoside phosphonate analogs, a class of novel antivirals structurally related to natural nucleotides (Fig. 1 ). (aspetjournals.org)
Yet risks of renal failure and renal replacement therapy were similar in patients treated with nucleoside analogues versus nucleotide analogues in real-life setting. (medscape.com)
These agents are classified according to their chemical structures: the three nucleoside analogues include lamivudine, telbivudine and entecavir, whereas the two nucleotide analogues include adefovir dipivoxil, tenofovir disoproxil fumarate (TDF), [ 2 ] and the newly approved tenofovir alafenamide (TAF). (medscape.com)

Pyrimidines are the nucleotide bases of deoxyribonu-cleic acid (DNA). (encyclopedia.com)

Tenofovir disoproxil is a diester pro-drug of the purine-based nucleotide analogue, tenofovir. (who.int)
Results Nephrotoxicity has been well reported in patients receiving older generations of nucleotide analogues, namely adefovir dipivoxil and tenofovir disoproxil fumarate (TDF). (medscape.com)

The NBDPS was a multisite, population-based, case-control study of genetic and non-genetic risk factors for major structural birth defects that included women with deliveries between 1997 and 2011. (cdc.gov)

Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP (2017) Nucleotide-time alignment for molecular recorders, PLoS Computational Biology 13(5):e1005483. (mit.edu)

Nucleotide excision repair. (news-medical.net)
Nucleotide excision repair is a widespread mechanism for repairing damage to DNA and recognizes multiple damaged bases. (news-medical.net)

The new nucleotide analogue, TAF is now available with favourable renal and bone safety profiles. (medscape.com)

In addition, a third conserved intronic sequence that is known to be functionally important in splicing is the so-called branch point site (BPS) which is usually located very close to the end of the intron, at most 40 nucleotides before the terminal dinucleotide. (ijbs.com)
There are at least two classes of pre-mRNA introns, based on the splicing machineries that catalyze the reaction. (ijbs.com)

It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse. (frontiersin.org)

The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder's rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder. (medlineplus.gov)
Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases. (medlineplus.gov)
DNA is a double helix formed by base pairs attached to a sugar-phosphate backbone. (medlineplus.gov)

Table 1: Enzymatic incorporation of fluorescent Nucleotides. (jenabioscience.com)
Damage to DNA is caused by the incorporation of incorrect nucleotide bases during DNA replication and the chemical changes caused by spontaneous mutation or exposure to environmental factors such as radiation. (news-medical.net)

These complementary bases are bonded together via hydrogen bonds, which can be easily broken apart when the DNA needs to unzip and duplicate itself. (knowgenetics.org)

Receptor-interacting protein kinase 2 (RIPK2) and nucleotide-binding oligomerization domain (NOD) cell signaling inhibitors based on a 3,5-diphenyl-2-aminopyridine scaffold. (ox.ac.uk)
A new class of RIPK2 kinase/NOD signaling inhibitors based on a 3,5-diphenyl-2-aminopyridine scaffold was developed. (ox.ac.uk)

Assembly provides versioned accession identifiers for submitted and RefSeq assemblies, links to the components in the Nucleotide system and direct access to the downloads on the NCBI FTP site. (nih.gov)
BioSample contains descriptions of biological source materials used in studies that have data in other NCBI molecular databases such as Assembly, Nucleotide and SRA. (nih.gov)

In version 2, BBB-v2, of Base-By-Base we have added a series of new features aimed at providing the bench virologist with a better platform to view, annotate and analyze these complex genomes. (biomedcentral.com)
The original version of Base-By-Base (BBB) [ 1 ] was developed by the Virus Bioinformatics Resource Center primarily because of a need for a customizable, platform-independent (Java), multiple sequence alignment (MSA) editor that could be used for the comparison, annotation and analysis of viral genomes, and also integrated directly with our MySQL database. (biomedcentral.com)

Generally, only a nucleotide variation that is found in more than 1% of the population is referred to as SNP. (jove.com)

Using our new profiles based on hydrophobicity properties we pointed out specific properties for regions surrounding splice sites. (ijbs.com)
In European-American and Asian regions where starch-based diets are common, the population shows a higher copy number of gene AMY1, a gene which is involved in starch metabolism. (jove.com)

Centers for Disease Control and Prevention, Fort Collins, Colo- nucleotide identity with ZIKV. (folkhalsomyndigheten.se)

Cleaving the linkage between TdT and the incorporated nucleotide releases the primer and allows subsequent extension. (nature.com)

Method 1 weighs each risk allele equally using a simple method of counting the number of risk alleles, whereas method 2 weighs each risk SNP differently based on its odds ratio. (johnshopkins.edu)

Receptor-interacting protein kinase 2 (RIPK2) is a key mediator of nucleotide-binding oligomerization domain (NOD) cell signaling that has been implicated in various chronic inflammatory conditions. (ox.ac.uk)

Bases are the part of DNA that stores information and gives DNA the ability to encode phenotype , a personâ€™s visible traits. (knowgenetics.org)

Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality), which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. (nih.gov)

Sperm intracellular cAMP levels depend on the activity of adenylyl cyclases, mostly SACY, though transmembrane-containing adenylyl cyclases are also present, and on the activity of cyclic nucleotide phosphodiesterases (PDE) whose role is to degrade cAMP into 5'-AMP. (plos.org)
Tandem mass spectrometry was used to identify the intracellular metabolites (cytokinin monophosphorylated, diphosphorylated, and triphosphorylated nucleotides) in riboside-treated cells. (cas.cz)

The vinca alkaloid agents are naturally occurring or semisynthetic nitrogenous bases that elicit their cytotoxic effects through tubulin-binding properties and disruption of microtubule function, which lead to metaphase arrest. (medscape.com)

The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)

A web-based search of all original articles about the impact of gene polymorphisms on toxicity and response to therapy in HNSCCs was done until September 2021 using international English language databases including Google Scholar, Scopus, PubMed and Web of science. (researchsquare.com)
Although NAs are generally safe and relatively free of major side effects, [ 10 ] nephrotoxicity and bone toxicity may occur in a small yet significant proportion of patients receiving older generations of nucleotide analogues, for example, adefovir and TDF. (medscape.com)

This relationship is called complementary base paring. (knowgenetics.org)

Bearing in mind that the performance and quality criteria expected from NGS in diagnostic or research settings are strikingly different, we have developed an Ion Torrent's PGM-based routine diagnostic procedure for BRCA1/2 sequencing. (nih.gov)

A nucleotide is the basic structural unit and building block for DNA . (knowgenetics.org)

the direct reversal of the chemical process generating the damage and the replacement of damaged nucleotide bases. (news-medical.net)

Cancer chemotherapy is based on an understanding of tumor cell growth and of how drugs affect this growth. (medscape.com)

The statistical power of our double-blind approach is demonstrated in the flagging of mathematical functional correlations of SNP information-based potentials in multiple populations with specific environmental parameters. (scirp.org)
Base-By-Base is a Java-based multiple sequence alignment editor. (biomedcentral.com)

Anatomy7

Organisms11

Diseases3

Chemicals and Drugs118

Analytical, Diagnostic and Therapeutic Techniques and Equipment31

Phenomena and Processes93

Information Science5

Health Care4

SNPs10

Sequences9

Genome5

Substitutions3

Cyclic Nucleotide Phosphodiesterase1

Single23

Guanine4

Adenine1

Variations2

Amino2

Phosphate group2

Strands2

Polymerase3

Synthesis1

Nucleoside3

Pyrimidines1

Tenofovir2

Genetic1

20171

Excision2

Analogue1

Splicing2

Genomic1

Double helix3

Incorporation2

Hydrogen bonds1

Inhibitors2

NCBI2

Genomes2

Variation1

Regions2

Disease1

Primer1

Odds Ratio1

Protein kinase1

Traits1

Variant1

Intracellular2

Nitrogenous Bases1

Deletion1

Toxicity2

Complementary base1

BRCA11

Structural1

Chemical1

Tumor1

Multiple2