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Pre-B-cell leukemia transcription factor 1 is a protein that in humans is encoded by the PBX1 gene. The homologous protein in Drosophila is known as extradenticle, and causes changes in embryonic development.
Function
Mice studies suggest PBX1 is involved in bone generation and skeletal patterning
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https://huggingface.co/datasets/fmars/wiki_stem
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Pre-B-cell leukemia transcription factor 2 is a protein that in humans is encoded by the PBX2 gene.
Function
This gene encodes a ubiquitously expressed member of the TALE/PBX homeobox family. It was identified by its similarity to a homeobox gene which is involved in t(1;19) translocation in acute pre-B-cell leukemias
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https://huggingface.co/datasets/fmars/wiki_stem
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PDX1 (pancreatic and duodenal homeobox 1), also known as insulin promoter factor 1, is a transcription factor in the ParaHox gene cluster. In vertebrates, Pdx1 is necessary for pancreatic development, including β-cell maturation, and duodenal differentiation. In humans this protein is encoded by the PDX1 gene, which was formerly known as IPF1
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https://huggingface.co/datasets/fmars/wiki_stem
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PER2 is a protein in mammals encoded by the PER2 gene. PER2 is noted for its major role in circadian rhythms.
Discovery
The per gene was first discovered using forward genetics in Drosophilla melanogaster in 1971
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https://huggingface.co/datasets/fmars/wiki_stem
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The PER3 gene encodes the period circadian protein homolog 3 protein in humans. PER3 is a paralog to the PER1 and PER2 genes. It is a circadian gene associated with delayed sleep phase syndrome in humans
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https://huggingface.co/datasets/fmars/wiki_stem
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Peroxisome proliferator-activated receptor alpha (PPAR-α), also known as NR1C1 (nuclear receptor subfamily 1, group C, member 1), is a nuclear receptor protein functioning as a transcription factor that in humans is encoded by the PPARA gene. Together with peroxisome proliferator-activated receptor delta and peroxisome proliferator-activated receptor gamma, PPAR-alpha is part of the subfamily of peroxisome proliferator-activated receptors. It was the first member of the PPAR family to be cloned in 1990 by Stephen Green and has been identified as the nuclear receptor for a diverse class of rodent hepatocarcinogens that causes proliferation of peroxisomes
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https://huggingface.co/datasets/fmars/wiki_stem
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Peroxisome proliferator-activated receptor delta (PPAR-delta), or (PPAR-beta), also known as Nuclear hormone receptor 1 (NUC1) is a nuclear receptor that in humans is encoded by the PPARD gene. This gene encodes a member of the peroxisome proliferator-activated receptor (PPAR) family. It was first identified in Xenopus in 1993
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https://huggingface.co/datasets/fmars/wiki_stem
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Peroxisome proliferator- activated receptor gamma (PPAR-γ or PPARG), also known as the glitazone reverse insulin resistance
receptor, or NR1C3 (nuclear receptor subfamily 1, group C, member 3) is a type II nuclear receptor functioning as a transcription factor that in humans is encoded by the PPARG gene.
Tissue distribution
PPARG is mainly present in adipose tissue, colon and macrophages. Two isoforms of PPARG are detected in the human and in the mouse: PPAR-γ1 (found in nearly all tissues except muscle) and PPAR-γ2 (mostly found in adipose tissue and the intestine)
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https://huggingface.co/datasets/fmars/wiki_stem
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PHD finger protein 1 is a protein that in humans is encoded by the PHF1 gene.
Function
This gene encodes a protein with significant sequence similarity to Drosophila Polycomblike. The encoded protein contains a zinc finger-like PHD (plant homeodomain) finger which is distinct from other classes of zinc finger motifs and which shows the typical Cys4-His-Cys3 arrangement
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https://huggingface.co/datasets/fmars/wiki_stem
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PHD finger protein 8 is a protein that in humans is encoded by the PHF8 gene.
Function
PHF8 belongs to the family of ferrous iron and alpha-ketoglutarate-dependent hydroxylases superfamily. , and is active as a histone lysine demethylase with selectivity for the di-and monomethyl states
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https://huggingface.co/datasets/fmars/wiki_stem
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PHD finger protein 10 is a protein that in humans is encoded by the PHF10 gene.
Function
This gene contains a predicted ORF that encodes a protein with two zinc finger domains. The function of the encoded protein is not known
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https://huggingface.co/datasets/fmars/wiki_stem
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Protein Jade-3 is a protein that in humans is encoded by the PHF16 gene. This gene is part of a gene cluster on chromosome Xp11. 23
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https://huggingface.co/datasets/fmars/wiki_stem
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PHD finger protein 21A is a protein that in humans is encoded by the PHF21A gene.
Function
BHC80 is a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al. , 2002)
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https://huggingface.co/datasets/fmars/wiki_stem
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Pho4 is a protein with a basic helix-loop-helix (bHLH) transcription factor. It is found in S. cerevisiae and other yeasts
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https://huggingface.co/datasets/fmars/wiki_stem
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The photoreceptor cell-specific nuclear receptor (PNR), also known as NR2E3 (nuclear receptor subfamily 2, group E, member 3), is a protein that in humans is encoded by the NR2E3 gene. PNR is a member of the nuclear receptor super family of intracellular transcription factors.
Function
PNR is exclusively expressed in the retina
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https://huggingface.co/datasets/fmars/wiki_stem
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Paired mesoderm homeobox protein 2A is a protein that in humans is encoded by the PHOX2A gene.
Function
The protein encoded by this gene contains a paired-like homeodomain most similar to that of the Drosophila aristaless gene product. This protein is expressed specifically in noradrenergic cell types
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https://huggingface.co/datasets/fmars/wiki_stem
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Paired-like homeobox 2b (PHOX2B), also known as neuroblastoma Phox (NBPhox), is a protein that in humans is encoded by the PHOX2B gene located on chromosome 4. It codes for a homeodomain transcription factor. It is expressed exclusively in the nervous system, in most neurons that control the viscera (cardiovascular, digestive and respiratory systems)
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https://huggingface.co/datasets/fmars/wiki_stem
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Paired-like homeodomain transcription factor 2 also known as pituitary homeobox 2 is a protein that in humans is encoded by the PITX2 gene.
Function
This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. This protein acts as a transcription factor and regulates procollagen lysyl hydroxylase gene expression
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https://huggingface.co/datasets/fmars/wiki_stem
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Pituitary homeobox 3 is a protein that in humans is encoded by the PITX3 gene.
Function
This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family act as transcription factors
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https://huggingface.co/datasets/fmars/wiki_stem
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PBX/Knotted 1 Homeobox 1 (PKNOX1) is a protein that in humans is encoded by the PKNOX1 gene. An important paralog of this gene is PKNOX2.
Function
PKNOX1 belongs to the three amino acid loop extension (TALE) class of homeodomain transcription factors that form transcriptionally active complexes involved in development and organogenesis
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https://huggingface.co/datasets/fmars/wiki_stem
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PBX/Knotted 1 Homeobox 2 (PKNOX2) protein belongs to the three amino acid loop extension (TALE) class of homeodomain proteins, and is encoded by PKNOX2 gene in humans. The protein regulates the transcription of other genes and affects anatomical development.
Function
PKNOX2 protein regulates expression of other genes by binding to DNA in a sequence-specific manner, i
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https://huggingface.co/datasets/fmars/wiki_stem
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Zinc finger protein PLAG1 is a protein that in humans is encoded by the PLAG1 gene.
Function
Pleomorphic adenoma gene 1 encodes a zinc finger protein with 2 putative nuclear localization signals. PLAG1, which is developmentally regulated, has been shown to be consistently rearranged in pleomorphic adenomas of the salivary glands
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https://huggingface.co/datasets/fmars/wiki_stem
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PPAR agonists are drugs which act upon the peroxisome proliferator-activated receptor. They are used for the treatment of symptoms of the metabolic syndrome, mainly for lowering triglycerides and blood sugar.
Classification
PPAR-alpha and PPAR-gamma are the molecular targets of a number of marketed drugs
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https://huggingface.co/datasets/fmars/wiki_stem
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PR domain zinc finger protein 2 is a protein that in humans is encoded by the PRDM2 gene.
Function
This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene
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https://huggingface.co/datasets/fmars/wiki_stem
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PR domain zinc finger protein 9 is a protein that in humans is encoded by the PRDM9 gene. PRDM9 is responsible for positioning recombination hotspots during meiosis by binding a DNA sequence motif encoded in its zinc finger domain. PRDM9 is the only speciation gene found so far in mammals, and is one of the fastest evolving genes in the genome
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https://huggingface.co/datasets/fmars/wiki_stem
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PR domain containing 16, also known as PRDM16, is a protein which in humans is encoded by the PRDM16 gene. PRDM16 acts as a transcription coregulator that controls the development of brown adipocytes in brown adipose tissue. Previously, this coregulator was believed to be present only in brown adipose tissue, but more recent studies have shown that PRDM16 is highly expressed in subcutaneous white adipose tissue as well
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https://huggingface.co/datasets/fmars/wiki_stem
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The progesterone receptor (PR), also known as NR3C3 or nuclear receptor subfamily 3, group C, member 3, is a protein found inside cells. It is activated by the steroid hormone progesterone.
In humans, PR is encoded by a single PGR gene residing on chromosome 11q22, it has two isoforms, PR-A and PR-B, that differ in their molecular weight
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https://huggingface.co/datasets/fmars/wiki_stem
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Homeobox protein prophet of PIT-1 is a protein that in humans is encoded by the PROP1 gene. PROP1 has both DNA-binding and transcriptional activation ability. Its expression leads to ontogenesis of pituitary gonadotropes, as well as somatotropes, lactotropes, and caudomedial thyrotropes
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https://huggingface.co/datasets/fmars/wiki_stem
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Protein AATF, also known as apoptosis-antagonizing transcription factor is a protein that in humans is encoded by the AATF gene.
Function
The protein encoded by this gene was identified on the basis of its interaction with MAP3K12/DLK, a protein kinase known to be involved in the induction of cell apoptosis. This gene product contains a leucine zipper, which is a characteristic motif of transcription factors, and was shown to exhibit strong transactivation activity when fused to Gal4 DNA binding domain
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https://huggingface.co/datasets/fmars/wiki_stem
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Gavino Gulia (1835–1889) was a Maltese botanist and author of books on flora of that island.
References
Obituary in: "Obituary Notes" . Popular Science Monthly
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Tumour mutational burden (abbreviated as TMB) is a genetic characteristic of tumorous tissue that can be informative to cancer research and treatment. It is defined as the number of non-inherited mutations per million bases (Mb) of investigated genomic sequence, and its measurement has been enabled by next generation sequencing. TMB has shown potential as a predictive biomarker with several applications, including associations reported between different TMB levels and patient response to immune checkpoint inhibitor (ICI) therapy in a variety of cancers
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https://huggingface.co/datasets/fmars/wiki_stem
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V600E is a mutation of the BRAF gene in which valine (V) is substituted by glutamic acid (E) at amino acid 600. It is a driver mutation in a proportion of certain diagnoses, including melanoma, hairy cell leukemia, papillary thyroid carcinoma, colorectal cancer, non-small-cell lung cancer, Langerhans cell histiocytosis, Erdheim–Chester disease (a non-Langerhans-cell histiocytosis) and ameloblastoma. The mechanism of the mutation is that the negative charge of the acidic glutamic acid residue causes it to be phosphomimetic
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https://huggingface.co/datasets/fmars/wiki_stem
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Worm bagging (also referred to as facultative vivipary or endotokia matricida) is a form of vivipary observed in nematodes, namely Caenorhabditis elegans. The process is characterized by eggs hatching within the parent and the larvae proceeding to consume and emerge from the parent.
History
While the phenomenon was mentioned as a result of fluorodeoxyuridine treatment as early as 1979 and egg-laying mutants were identified in 1984, the natural circumstances and mechanisms resulting in this behavior were not fully explored until 2003
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Nucleobases (nitrogenous bases or simply bases) are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical
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Nucleic acid analogues are compounds which are analogous (structurally similar) to naturally occurring RNA and DNA, used in medicine and in molecular biology research.
Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases.
An analogue may have any of these altered
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Adenine () (symbol A or Ade) is a purine nucleobase. It is one of the four nucleobases in the nucleic acids of DNA, the other three being guanine (G), cytosine (C), and thymine (T). Adenine derivatives have various roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD) and Coenzyme A
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5-Bromouracil (5-BrU, 5BrUra, or br5Ura) is a brominated derivative of uracil that acts as an antimetabolite or base analog, substituting for thymine in DNA, and can induce DNA mutation in the same way as 2-aminopurine. It is used mainly as an experimental mutagen, but its deoxyriboside derivative (5-bromo-2-deoxy-uridine) is used to treat neoplasms.
5-BrU exists in three tautomeric forms that have different base pairing properties
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Cytosine () (symbol C or Cyt) is one of the four nucleobases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine
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2,6-diaminopurine (2,6-DAP, also known as 2-aminoadenine) is a compound once used in the treatment of leukemia. As the Z base, it is found instead of adenine (A) in the genetic material of some bacteriophage viruses. In August 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting 2,6-diaminopurine and related organic molecules, including the DNA and RNA components adenine and guanine, may have been formed extraterrestrially in outer space
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Fluorouracil (5-FU, 5-fluorouracil), sold under the brand name Adrucil among others, is a cytotoxic chemotherapy medication used to treat cancer. By intravenous injection it is used for treatment of colorectal cancer, oesophageal cancer, stomach cancer, pancreatic cancer, breast cancer, and cervical cancer. As a cream it is used for actinic keratosis, basal cell carcinoma, and skin warts
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Guanine () (symbol G or Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine
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5-Formylcytosine (5fC) is a pyrimidine nitrogen base derived from cytosine. In the context of nucleic acid chemistry and biology, it is regarded as an epigenetic marker. Discovered in 2011 in mammalian embryonic stem cells by Thomas Carell's research group the modified nucleoside was more recently confirmed to be relevant both as an intermediate in the active demethylation pathway and as a standalone epigenetic marker
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5-Hydroxymethylcytosine (5hmC) is a DNA pyrimidine nitrogen base derived from cytosine. It is potentially important in epigenetics, because the hydroxymethyl group on the cytosine can possibly switch a gene on and off. It was first seen in bacteriophages in 1952
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Hypoxanthine is a naturally occurring purine derivative. It is occasionally found as a constituent of nucleic acids, where it is present in the anticodon of tRNA in the form of its nucleoside inosine. It has a tautomer known as 6-hydroxypurine
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Isocytosine or 2-aminouracil is a pyrimidine base that is an isomer of cytosine. It is used in combination with isoguanine in studies of unnatural nucleic acid analogues of the normal base pairs in DNA. In particular, it is used as a nucleobase of hachimoji RNA
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Isoguanine or 2-hydroxyadenine is a purine base that is an isomer of guanine. It is a product of oxidative damage to DNA and has been shown to cause mutation. It is also used in combination with isocytosine in studies of unnatural nucleic acid analogues of the normal base pairs in DNA
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1-Methylcytosine is a methylated form of the DNA base cytosine.
In 1-methylcytosine, a methyl group is attached to the 1st atom in the 6-atom ring. This methyl group distinguishes 1-methylcytosine from cytosine
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https://huggingface.co/datasets/fmars/wiki_stem
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5-Methylcytosine is a methylated form of the DNA base cytosine (C) that regulates gene transcription and takes several other biological roles. When cytosine is methylated, the DNA maintains the same sequence, but the expression of methylated genes can be altered (the study of this is part of the field of epigenetics). 5-Methylcytosine is incorporated in the nucleoside 5-methylcytidine
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6-O-Methylguanine is a derivative of the nucleobase guanine in which a methyl group is attached to the oxygen atom. It base-pairs to thymine rather than cytosine, causing a G:C to A:T transition in DNA.
Formation
6-O-Methylguanine is formed in DNA by alkylation of the oxygen atom of guanine, most often by N-nitroso compounds (NOC) and sometimes due to methylation by other compounds such as endogenous S-adenosyl methionine
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7-Methylguanine is a modified purine nucleobase. It is a methylated version of guanine. The 7-methylguanine nucleoside is called 7-methylguanosine
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Propylthiouracil (PTU) is a medication used to treat hyperthyroidism. This includes hyperthyroidism due to Graves' disease and toxic multinodular goiter. In a thyrotoxic crisis it is generally more effective than methimazole
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Queuine () (Q) is a hypermodified nucleobase found in the first (or wobble) position of the anticodon of tRNAs specific for Asn, Asp, His, and Tyr, in most eukaryotes and prokaryotes. Because it is utilized by all eukaryotes but produced exclusively by bacteria, it is a putative vitamin. The nucleoside of queuine is queuosine
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2-Thiouracil is a specific molecule consisting of a sulfated uracil.
Medical use
The substance is a historically relevant anti-thyroid preparation. Astwood E
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Thymine () (symbol T or Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase
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Tioguanine, also known as thioguanine or 6-thioguanine (6-TG) is a medication used to treat acute myeloid leukemia (AML), acute lymphocytic leukemia (ALL), and chronic myeloid leukemia (CML). Long-term use is not recommended. It is given by mouth
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Uracil () (symbol U or Ura) is one of the four nucleobases in the nucleic acid RNA. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds
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Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver
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Adenosine 5′-tetraphosphate, Ap4 or ATPP is a nucleotide. It is produced from ATP and triphosphate (P3) through the action of acetyl—CoA synthetase. Acetyl—CoA synthetase also produces adenosine 5'-pentaphosphate through the reaction of ADP and tetraphosphate (P4)
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Adenosine diphosphate ribose (ADPR) is an ester molecule formed into chains by the enzyme poly ADP ribose polymerase. ADPR is created from cyclic ADP-ribose (cADPR) by the CD38 enzyme using nicotinamide adenine dinucleotide (NAD+) as a cofactor. ADPR binds to and activates the TRPM2 ion channel
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Adenosine monophosphate (AMP), also known as 5'-adenylic acid, is a nucleotide. AMP consists of a phosphate group, the sugar ribose, and the nucleobase adenine. It is an ester of phosphoric acid and the nucleoside adenosine
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Adenosine diphosphate (ADP), also known as adenosine pyrophosphate (APP), is an important organic compound in metabolism and is essential to the flow of energy in living cells. ADP consists of three important structural components: a sugar backbone attached to adenine and two phosphate groups bonded to the 5 carbon atom of ribose. The diphosphate group of ADP is attached to the 5’ carbon of the sugar backbone, while the adenine attaches to the 1’ carbon
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Adenosine triphosphate (ATP) is an organic compound that provides energy to drive and support many processes in living cells, such as muscle contraction, nerve impulse propagation, condensate dissolution, and chemical synthesis. Found in all known forms of life, ATP is often referred to as the "molecular unit of currency" of intracellular energy transfer. When consumed in metabolic processes, it converts either to adenosine diphosphate (ADP) or to adenosine monophosphate (AMP)
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Adenosine thiamine triphosphate (AThTP), or thiaminylated adenosine triphosphate, is a natural thiamine adenine nucleotide. It was discovered in Escherichia coli where it may account for up to 15 - 20% of total thiamine under carbon starvation. AThTP also exists in eukaryotic organisms such as yeast, roots of higher plants and animal tissues, albeit at a much lower concentration
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5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR) is an intermediate in the generation of inosine monophosphate. AICAR is an analog of adenosine monophosphate (AMP) that is capable of stimulating AMP-dependent protein kinase (AMPK) activity. The drug has also been shown as a potential treatment for diabetes by increasing the metabolic activity of tissues by changing the physical composition of muscle
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Aminoallyl nucleotide is a nucleotide with a modified base containing an allylamine. They are used in post-labeling of nucleic acids by fluorescence detection in microarray. They are reactive with N-Hydroxysuccinimide ester group which helps attach a fluorescent dye to the primary amino group on the nucleotide
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5′-Phosphoribosyl-5-aminoimidazole (or aminoimidazole ribotide, AIR) is a biochemical intermediate in the formation of purine nucleotides via inosine-5-monophosphate, and hence is a building block for DNA and RNA. The vitamins thiamine and cobalamin also contain fragments derived from AIR. It is an intermediate in the adenine pathway and is synthesized from 5′-phosphoribosylformylglycinamidine by AIR synthetase
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Diadenosine tetraphosphate or Ap4A is a putative alarmone, ubiquitous in nature being common to everything from bacteria to humans. It is made up of two adenosines joined together by a 5′-5′ linked chain of four phosphates. Adenosine polyphosphates are capable of inducing multiple physiological effects
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A bridged nucleic acid (BNA) is a modified RNA nucleotide. They are sometimes also referred to as constrained or inaccessible RNA molecules. BNA monomers can contain a five-membered, six-membered or even a seven-membered bridged structure with a "fixed" C3'-endo sugar puckering
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Bucladesine is a cyclic nucleotide derivative which mimics the action of endogenous cAMP and is a phosphodiesterase inhibitor.
Bucladesine is a cell permeable cAMP analog. The compound is used in a wide variety of research applications because it mimics cAMP and can induce normal physiological responses when added to cells in experimental conditions
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Cangrelor, sold under the brand name Kengreal among others, is a P2Y12 inhibitor FDA approved as of June 2015 as an antiplatelet drug for intravenous application. Some P2Y12 inhibitors are used clinically as effective inhibitors of adenosine diphosphate-mediated platelet activation and aggregation. Unlike clopidogrel (Plavix), which is a prodrug, cangrelor is an active drug not requiring metabolic conversion
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Citicoline (INN), also known as cytidine diphosphate-choline (CDP-Choline) or cytidine 5'-diphosphocholine is an intermediate in the generation of phosphatidylcholine from choline, a common biochemical process in cell membranes. Citicoline is naturally occurring in the cells of human and animal tissue, in particular the organs.
Use as a dietary supplement
Citicoline is available as a supplement in over 70 countries under a variety of brand names: Cebroton, Ceraxon, Cidilin, Citifar, Cognizin, Difosfocin, Hipercol, NeurAxon, Nicholin, Sinkron, Somazina, Synapsine, Startonyl, Trausan, Xerenoos, etc
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Cyclic adenosine monophosphate (cAMP, cyclic AMP, or 3',5'-cyclic adenosine monophosphate) is a second messenger, or cellular signal occurring within cells, that is important in many biological processes. cAMP is a derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.
History
Earl Sutherland of Vanderbilt University won a Nobel Prize in Physiology or Medicine in 1971 "for his discoveries concerning the mechanisms of the action of hormones", especially epinephrine, via second messengers (such as cyclic adenosine monophosphate, cyclic AMP)
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Cyclic ADP Ribose, frequently abbreviated as cADPR, is a cyclic adenine nucleotide (like cAMP) with two phosphate groups present on 5' OH of the adenosine (like ADP), further connected to another ribose at the 5' position, which, in turn, closes the cycle by glycosidic bonding to the nitrogen 1 (N1) of the same adenine base (whose position N9 has the glycosidic bond to the other ribose). The N1-glycosidic bond to adenine is what distinguishes cADPR from ADP-ribose (ADPR), the non-cyclic analog. cADPR is produced from nicotinamide adenine dinucleotide (NAD+) by ADP-ribosyl cyclases (EC 3
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Cyclic di-AMP (also called c-di-AMP and c-di-adenosine monophosphate) is a second messenger used in signal transduction in bacteria and archaea. It is present in many Gram-positive bacteria, some Gram-negative species, and archaea of the phylum euryarchaeota.
It is one of many ubiquitous nucleotide second messengers including cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), guanosine pentaphosphate ((p)ppGpp), and cyclic di-GMP (c-di-GMP)
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https://huggingface.co/datasets/fmars/wiki_stem
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Cyclic di-GMP (also called cyclic diguanylate and c-di-GMP) is a second messenger used in signal transduction in a wide variety of bacteria. Cyclic di-GMP is not known to be used by archaea, and has only been observed in eukaryotes in Dictyostelium. The biological role of cyclic di-GMP was first uncovered when it was identified as an allosteric activator of a cellulose synthase found in Gluconacetobacter xylinus in order to produce microbial cellulose
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https://huggingface.co/datasets/fmars/wiki_stem
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Cyclic guanosine monophosphate–adenosine monophosphate (cyclic GMP-AMP, cGAMP) is the first cyclic di-nucleotide found in metazoa.
In mammalian cells, cGAMP is synthesized by cyclic GMP-AMP synthase (cGAS) from ATP and GTP upon cytosolic DNA stimulation. cGAMP produced by cGAS contains mixed phosphodiester linkages, with one between 2'-OH of GMP and 5'-phosphate of AMP and the other between 3'-OH of AMP and 5'-phosphate of GMP
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https://huggingface.co/datasets/fmars/wiki_stem
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Cyclic guanosine monophosphate (cGMP) is a cyclic nucleotide derived from guanosine triphosphate (GTP). cGMP acts as a second messenger much like cyclic AMP. Its most likely mechanism of action is activation of intracellular protein kinases in response to the binding of membrane-impermeable peptide hormones to the external cell surface
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https://huggingface.co/datasets/fmars/wiki_stem
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A cyclic nucleotide (cNMP) is a single-phosphate nucleotide with a cyclic bond arrangement between the sugar and phosphate groups. Like other nucleotides, cyclic nucleotides are composed of three functional groups: a sugar, a nitrogenous base, and a single phosphate group. As can be seen in the cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) images, the 'cyclic' portion consists of two bonds between the phosphate group and the 3' and 5' hydroxyl groups of the sugar, very often a ribose
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https://huggingface.co/datasets/fmars/wiki_stem
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Cytidine monophosphate, also known as 5'-cytidylic acid or simply cytidylate, and abbreviated CMP, is a nucleotide that is used as a monomer in RNA. It is an ester of phosphoric acid with the nucleoside cytidine. CMP consists of the phosphate group, the pentose sugar ribose, and the nucleobase cytosine; hence, a ribonucleoside monophosphate
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https://huggingface.co/datasets/fmars/wiki_stem
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Cytidine triphosphate (CTP) is a pyrimidine nucleoside triphosphate. CTP, much like ATP, consists of a ribose sugar, and three phosphate groups. The major difference between the two molecules is the base used, which in CTP is cytosine
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https://huggingface.co/datasets/fmars/wiki_stem
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Denufosol (INN) is an inhaled drug for the treatment of cystic fibrosis, being developed by Inspire Pharmaceuticals and sponsored by the Cystic Fibrosis Foundation. It was tested in two Phase III clinical trials, TIGER-1 and TIGER-2. Initially, in the first Phase III trial, TIGER-1, the compound showed significant results as compared with placebo
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https://huggingface.co/datasets/fmars/wiki_stem
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Deoxyadenosine triphosphate (dATP) is a nucleotide used in cells for DNA synthesis (or replication), as a substrate of DNA polymerase. Deoxyadenosine triphosphate is produced from DNA by the action of nuclease P1, adenylate kinase, and pyruvate kinase.
Health effects
High levels of dATP can be toxic and result in impaired immune function, since dATP acts as a noncompetitive inhibitor for the DNA synthesis enzyme ribonucleotide reductase
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https://huggingface.co/datasets/fmars/wiki_stem
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Deoxycytidine diphosphate is a nucleoside diphosphate. It is related to the common nucleic acid CTP, or cytidine triphosphate, with the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name), and with one fewer phosphoryl group than CTP .
2'-deoxycytidine diphosphate is abbreviated as dCDP
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https://huggingface.co/datasets/fmars/wiki_stem
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Deoxycytidine triphosphate (dCTP) is a nucleoside triphosphate that contains the pyrimidine base cytosine. The triphosphate group contains high-energy phosphoanhydride bonds, which liberate energy when hydrolized.
DNA polymerase enzymes use this energy to incorporate deoxycytidine into a newly synthesized strand of DNA
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https://huggingface.co/datasets/fmars/wiki_stem
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A deoxyribonucleotide is a nucleotide that contains deoxyribose. They are the monomeric units of the informational biopolymer, deoxyribonucleic acid (DNA). Each deoxyribonucleotide comprises three parts: a deoxyribose sugar (monosaccharide), a nitrogenous base, and one phosphoryl group
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https://huggingface.co/datasets/fmars/wiki_stem
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Disodium guanylate, also known as sodium 5'-guanylate and disodium 5'-guanylate, is a natural sodium salt of the flavor enhancing nucleotide guanosine monophosphate (GMP). Disodium guanylate is a food additive with the E number E627. It is commonly used in conjunction with glutamic acid
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https://huggingface.co/datasets/fmars/wiki_stem
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Disodium inosinate (E631) is the disodium salt of inosinic acid with the chemical formula C10H11N4Na2O8P. It is used as a food additive and often found in instant noodles, potato chips, and a variety of other snacks.
Commercial disodium inosinate may either be obtained from bacterial fermentation of sugars or prepared from animal products
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https://huggingface.co/datasets/fmars/wiki_stem
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In biochemistry, flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins, which is involved with several enzymatic reactions in metabolism. A flavoprotein is a protein that contains a flavin group, which may be in the form of FAD or flavin mononucleotide (FMN). Many flavoproteins are known: components of the succinate dehydrogenase complex, α-ketoglutarate dehydrogenase, and a component of the pyruvate dehydrogenase complex
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https://huggingface.co/datasets/fmars/wiki_stem
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GC skew is when the nucleotides guanine and cytosine are over- or under-abundant in a particular region of DNA or RNA. GC skew is also a statistical method for measuring strand-specific guanine overrepresentation. In equilibrium conditions (without mutational or selective pressure and with nucleotides randomly distributed within the genome) there is an equal frequency of the four DNA bases (adenine, guanine, thymine, and cytosine) on both single strands of a DNA molecule
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https://huggingface.co/datasets/fmars/wiki_stem
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Glycineamide ribonucleotide (or GAR) is a biochemical intermediate in the formation of purine nucleotides via inosine-5-monophosphate, and hence is a building block for DNA and RNA. The vitamins thiamine and cobalamin also contain fragments derived from GAR.
GAR is the product of the enzyme phosphoribosylamine—glycine ligase acting on phosphoribosylamine (PRA) to combine it with glycine in a process driven by ATP
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https://huggingface.co/datasets/fmars/wiki_stem
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GTPgammaS (GTPγS, guanosine 5'-O-[gamma-thio]triphosphate) is a non-hydrolyzable or slowly hydrolyzable G-protein-activating analog of guanosine triphosphate (GTP). Many GTP binding proteins demonstrate activity when bound to GTP, and are inactivated via the hydrolysis of the phosphoanhydride bond that links the γ-phosphate to the remainder of the nucleotide, leaving a bound guanosine diphosphate (GDP) and releasing an inorganic phosphate. This usually occurs rapidly, and the GTP-binding protein can then only be activated by exchanging the GDP for a new GTP molecule
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https://huggingface.co/datasets/fmars/wiki_stem
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5'-Guanylyl imidodiphosphate (GDPNP) is a purine nucleotide. It is an analog of guanosine triphosphate in which one of the oxygen atoms is replaced with an amine, producing a non-hydrolyzable functional group. Guanylyl imidodiphosphate binds tightly to G-proteins in the presence of Mg2+
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https://huggingface.co/datasets/fmars/wiki_stem
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Hovlinc RNA is a self-cleaving ribozyme of about 168 nucleotides found in a very long noncoding RNA (vlincRNA) in humans, chimpanzees, and gorillas. The word "hovlinc" comes from "hominin vlincRNA-located" RNA. Hovlinc is only a fourth known case of a ribozyme in human
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https://huggingface.co/datasets/fmars/wiki_stem
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Inosine triphosphate (ITP) is an intermediate in the purine metabolism pathway, seen in the synthesis of ATP and GTP. It comprises an inosine nucleotide containing three phosphate groups esterified to the sugar moiety.
ITP results from deamination of ATP
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https://huggingface.co/datasets/fmars/wiki_stem
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Inosinic acid or inosine monophosphate (IMP) is a nucleotide (that is, a nucleoside monophosphate). Widely used as a flavor enhancer, it is typically obtained from chicken byproducts or other meat industry waste. Inosinic acid is important in metabolism
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https://huggingface.co/datasets/fmars/wiki_stem
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An internal ribosome entry site, abbreviated IRES, is an RNA element that allows for translation initiation in a cap-independent manner, as part of the greater process of protein synthesis. In eukaryotic translation, initiation typically occurs at the 5' end of mRNA molecules, since 5' cap recognition is required for the assembly of the initiation complex. The location for IRES elements is often in the 5'UTR, but can also occur elsewhere in mRNAs
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https://huggingface.co/datasets/fmars/wiki_stem
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In molecular biology, the NAD+ five-prime cap (NAD+ 5’ cap) refers to a molecule of nicotinamide adenine dinucleotide (NAD+), a nucleoside-containing metabolite, covalently bonded the 5’ end of cellular mRNA. While the more common methylated guanosine (m7G) cap is added to RNA by a capping complex that associates with RNA polymerase II (RNAP II), the NAD cap is added during transcriptional initiation by the RNA polymerase itself, acting as a non-canonical initiating nucleotide (NCIN). As such, while m7G capping can only occur in organisms possessing specialized capping complexes, because NAD capping is performed by RNAP itself, it is hypothesized to occur in most, if not all, organisms
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https://huggingface.co/datasets/fmars/wiki_stem
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5'-guanosyl-methylene-triphosphate (GDPCP) and 5'-adenosyl-methylene-triphosphate (ADPCP) are analogues of guanosine 5'-triphosphate (GTP) and adenosine 5'-triphosphate (ATP), which store chemical energy from metabolism in the cell. Hydrolysis of nucleoside triphosphates (NTPs) such as ATP and GTP yields energy, inorganic phosphate (Pi or PPi), and either NDP or NMP. GDPCP and ADPCP are not subject to hydrolysis under the same conditions as NTPs; it is this property which makes them useful in experiments in biochemistry and molecular biology
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https://huggingface.co/datasets/fmars/wiki_stem
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Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an adenine nucleobase and the other, nicotinamide
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https://huggingface.co/datasets/fmars/wiki_stem
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Nicotinamide adenine dinucleotide phosphate, abbreviated NADP+ or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle and lipid and nucleic acid syntheses, which require NADPH as a reducing agent ('hydrogen source'). NADPH is the reduced form of NADP+, the oxidized form. NADP+ is used by all forms of cellular life
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https://huggingface.co/datasets/fmars/wiki_stem
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