Amino acid seq nuclear proteins. Medical search. Frequent questions

This nuclear localization suggests that C11orf98 protein may have a function related to the expression and regulation of genes in the nucleus. (wikipedia.org)
Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. (nih.gov)
One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. (mdpi.com)
RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. (nature.com)
2020). The 25 ZmHsf as well as 22 ZmHsp70 (heat shock protein) genes were confirmed to respond to heat stress treatment, indicating that they have potential effects in heat stress response (Jiang et al. (grassius.org)
Among the nTARs, 146 share significant similarity with proteins that have been identified in other species suggesting that they are hitherto unidentified genes in C. graminicola . (biomedcentral.com)
We successfully employed deep sequencing RNA-Seq data in combination with an elaborate bioinformatics strategy in order to identify novel genes, incorrect gene models and mechanisms of transcript processing in the corn anthracnose fungus C. graminicola . (biomedcentral.com)
ChIP-seq experiments in growing Tetrahymena show H3.3 enrichment over the promoters, gene bodies, and transcription termination sites of highly transcribed genes. (biomedcentral.com)
H3.3 knockout followed by RNA-seq reveals large-scale transcriptional alterations in functionally important genes. (biomedcentral.com)
The transcriptomic and epigenomic regulatory landscape of the MAC genome, which has 80% protein-coding genes and short intergenic regions, is poorly understood. (uni-frankfurt.de)
Most eukaryotes have at least six genes encoding SMC proteins (each 110-170 kDa, with a central hinge region and N- and C-terminal globular domains with Walker A and Walker B motifs forming the ATPase head domain). (pberghei.eu)
Recently, we elucidated the developmental role of tobacco ( Nicotiana tabacum L.) NtTTG2 in association with 12 genes that putatively encode AUXIN RESPONSIVE FACTOR (ARF) proteins, including NtARF8, NtARF17, and NtARF19. (biomedcentral.com)
We investigate the functional relevance of de novo missense variants, specifically whether they are likely to disrupt protein interactions, and nominate novel genes in risk for ASD through integrated genomic, transcriptomic, and proteomic analyses. (springer.com)
Finally, we integrate protein interactions and cell-type-specific co-expression networks together with published association data to implicate novel genes in ASD risk in a cell-type-specific manner. (springer.com)
Genes encoding disrupted complementary interactors tend to be risk genes, and an interaction network built from these proteins is enriched for ASD proteins. (springer.com)
Consistent with other studies, genes identified by disrupted protein interactions are expressed early in development and in excitatory and inhibitory neuronal lineages. (springer.com)
Using the newly released and larger ASC dataset, we confirm these observations and take them in several new directions: (1) By defining a set of genes encoding these disrupted protein interactors in ASD subjects and another for their siblings, we evaluate their expression patterns in developing brain from fetal to early postnatal development and within general cell types of brain tissue. (springer.com)
Ribonucleic acid (RNA) has multiple roles in cellular functions, from coding genes to non-coding regulatory activities. (biomedcentral.com)
Two genes encoding putative internalin proteins were chosen for further study. (omictools.com)
mRNA (messenger RNA): transfers information from the genes to the ribosome where proteins are made. (iitm.ac.in)
Jensen-Shannon and Grantham scores were computed for mutations in protein-coding genes to evaluate whether they affected protein function. (cdc.gov)

TTGs are characterized by the presence of the WD40 motif, which comprises the conserved tryptophan (W) and aspartic (D) dipeptide within a length of approximately 40 amino acid residues [ 6 - 11 ]. (biomedcentral.com)
We have identified a cytosolic acyl-CoA binding protein, with highly conserved amino acid residues and a typical acyl-CoA binding domain in N. caninum . (biomedcentral.com)

The carbohydrate-active enzymes database (CAZy", NUCLEIC ACIDS RES. (sumobrain.com)
Nucleic Acids Res, 2003 Aug 15. (nih.gov)

Can I use NGS data from other projects, such as exome-seq, RNA-seq, ChIP-seq, or ATAC-seq, for mtDNA sequence analysis? (northwestern.edu)

One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)
In most eukaryotes, two classes of histones have been described: (1) replicative or canonical histones, expressed only during the S phase of the cell cycle, which are assembled onto chromatin in a DNA replication-dependent (RD) manner, and (2) variant histones, which differ in their primary amino acid sequences, are expressed throughout the cell cycle, and can be deposited in a replication-independent (RI) fashion [ 2 ]. (biomedcentral.com)
In eukaryotic cells, chromatin comprises a complex consisting of DNA, RNA, and proteins where covalent modifications correlate with regulation of gene expression [ 1 ]. (biomedcentral.com)
Using a recombinant endonuclease-deficient Cas9-based gene promoter pulldown approach coupled with mass spectrometry, we found that MCUb is upregulated in the T2D heart due to loss of glucose homeostasis regulator nuclear receptor corepressor 2 repression, and chromatin immunoprecipitation assays identified peroxisome proliferator-activated receptor α as a mediator of MCUb gene expression in T2D cardiomyocytes. (diabetesjournals.org)
These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. (biomedcentral.com)
Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. (biomedcentral.com)

The IB1cDNA encodes a 714 amino acid protein with a proline-rich region and a putative basic helix-loop-helix domain (bHLH). (justia.com)

The c11orf98 gene encodes a protein that is 123 amino acids long. (wikipedia.org)
This gene encodes a 28S subunit protein. (nih.gov)
Ameiotic1 ( Am1 ) encodes a plant-specific nuclear protein (AM1) required for meiotic entry and progression through early prophase I. Pollen mother cells (PMCs) remain mitotic in most am1 mutants including am1-489 , while am1-praI permits meiotic entry but PMCs arrest at the leptotene/zygotene (L/Z) transition, defining the roles of AM1 protein in two distinct steps of meiosis. (biomedcentral.com)

Does the long-range PCR performed to enrich mtDNA from total gDNA amplify NUMTs (nuclear mitochondrial DNA sequences)? (northwestern.edu)
A hyperphosphorylated, ubiquitinated, and cleaved form of TDP43 known as pathologic TDP43 is the major disease protein in ubiquitin-positive, tau-, and alpha-synuclein-negative frontotemporal dementia (FLTD-U). TDP43 is not related to TRBP1, and RNA binding protein that binds HIV-1 TAR RNA sequences. (thermofisher.com)

Binding of the human homolog of the Drosophila discs large tumor suppressor protein to the mitochondrial ribosomal protein MRP-S34. (nih.gov)
First identified in Drosophila, the conserved Polycomb group (Pc-G) protein complexes were shown to be both writers (Polycomb Repressive Complex 2, PRC2) and readers (Polycomb Repressive Complex 1, PRC1) of H3K27me3 [ 19 , 20 , 21 ]. (biomedcentral.com)
The reversible conversion of constitutively expressed HSF to a form that can bind DNA requires the trimerization of the protein, involving leucine zipper interactions as shown for yeast, Drosophila, chicken and human HSFs. (grassius.org)

I aimed to identify RNA-binding proteins (RBPs) in yeast that associate with ER and to assess their role in mRNA localization and/or translation at ER. (uni-tuebingen.de)
Secondary, mRNA-seq analysis identified Gadd45 as a potential transcriptional target of dGLYAT, as depletion of dGLYAT decreased Gadd45 mRNA level. (sdbonline.org)
This protein is a specific component of the complex that includes pre-mRNA processing factors PRPF3, PRPF4, and PRPF18, as well as U4/U5/U6 tri-snRNP. (nih.gov)
tRNA (transfer RNA): decodes the information present in the mRNA and helps add amino acids to a protein chain. (iitm.ac.in)
TotalSeq™ is BioLegend's brand of antibody-oligonucleotide conjugates, to enable simultaneous analysis of proteins and mRNA in single cells. (biolegend.com)
CITE-seq and REAP-seq are two similar workflows for simultaneous protein and mRNA analysis, and the TotalSeq™ conjugates integrate seamlessly into these established protocols. (biolegend.com)

Mammalian mitochondrial ribosomal proteins (4). (nih.gov)
The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. (northwestern.edu)
Standard mtDNA-seq bioinformatics service includes sequencing data QC, alignment to the reference mitochondrial genome, and variant analysis. (northwestern.edu)
Nearly all DNA extraction kits or procedures purify both nuclear and mitochondrial DNA into the final product. (northwestern.edu)
Furthermore, GSOs protected cells against GLU-induced apoptosis by reducing the expression of the mitochondrial apoptosis-associated Bcl-2 family effector proteins and protected cells from GLU-induced oxidative damage by increasing the nuclear translocation of Nrf2 and HO-1 expression. (sdbonline.org)
Mitochondrial pellets were resuspended in PBS at a concentration ~1 mg total protein/mL. (nih.gov)
HEK293T expressing mitochondrial-targeted DsRed protein (Human Embryonic Kidney, pMitoDsRed, Clontech Laboratories) were generated as previously described (Miyata et al. (nih.gov)
In this study, we show that the T2D heart is metabolically inflexible and almost exclusively dependent on mitochondrial fatty acid oxidation as a consequence of mitochondrial calcium uniporter complex (MCUC) inhibitory subunit MCUb overexpression. (diabetesjournals.org)

Sumoylation is a post-translational modification involved in nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, response to stress, and progression through the cell cycle. (wikipedia.org)
TDP43 was first identified as a novel cellular protein that binds to HIV-1 virus TAR DNA sequence motifs and acts a transcriptional repressor to the HIV-1 LTR. (thermofisher.com)

Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. (nih.gov)
This, coupled with the very limited DNA damage repair capability in the organelle, leads to sequence alterations in mtDNA at a much higher frequency than that in the nuclear DNA. (northwestern.edu)
NUMTs are a result of insertion of mtDNA sequence into the nuclear genome. (northwestern.edu)
Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola . (biomedcentral.com)
An ORF is a theoretical aa-coding region, which is generally identified by analyzing the DNA nucleic acid sequence. (biomedcentral.com)
Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs. (omictools.com)
RNA therapies, on the other hand, make temporary changes on the output of a gene (the protein) instead of changing the actual sequence [1]. (iitm.ac.in)
The DYKDDDDK tag, commonly referred to as Sigma®'s FLAG® Tag, is often used as a protein modification in order to simplify the labeling and detection of proteins.This unique amino acid sequence allows for specific antibody detection in western blotting, immunoprecipitation, and immunostaining techniques.Due to the short sequence, this modification is not likely to affect the structure or function of the modified proteins. (biolegend.com)

Raised against amino acids 139-347 of recombinant human NFYA. (encodeproject.org)
The recombinant NcACBP protein was expressed to verify the binding activities of NcACBP in vitro , and the heterologous expression of NcACBP in Δacbp yeast in vivo . (biomedcentral.com)
The NcACBP recombinant protein was able to specifically bind acyl-CoA esters in vitro . (biomedcentral.com)

cell lines, these transcripts are translated into immunodetectable cytoplasmic and nuclear protein. (justia.com)
To validate the SMC4 subcellular location, fractionation of cytoplasmic and nuclear extracts derived from purified gametocytes revealed the presence of SMC4 in the nucleus. (pberghei.eu)

This is significant because this modification is exclusively found on nuclear and cytoplasmic proteins rather than membrane proteins and secretory proteins. (wikipedia.org)
The endoplasmic reticulum (ER) is the site of protein synthesis for secretory and membrane proteins. (uni-tuebingen.de)

Among the established custom DNA binding domains, Cas9 is most easily scaled to facilitate genome-scale perturbations 3 , 4 due to its simplicity of programming relative to zinc finger proteins and transcription activator-like effectors (TALEs). (cdc.gov)

They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. (nih.gov)
rRNA (ribosomal RNA): forms the primary component of ribosomes and catalyzes the assembly of amino acids into protein chains. (iitm.ac.in)

In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
An essential component of chromosome dynamics is a family of structural maintenance of chromosomes proteins, originally described in budding yeast as stability of minichromosomes (SMC) proteins, which are implicated in chromosome segregation and condensation. (pberghei.eu)

Utilizing our previous interactome perturbation predictor, we identify a set of missense variants that are likely disruptive to protein-protein interactions. (springer.com)
Extending earlier work, we show that de novo missense variants that disrupt protein interactions are enriched in individuals with ASD, often affecting hub proteins and disrupting hub interactions. (springer.com)
Disrupted protein interactions identify gene sets involved in risk for ASD. (springer.com)
This protein has been shown to possess PPIase activity and may act as a protein chaperone that mediates the interactions between different proteins inside the spliceosome. (nih.gov)

Increased levels of mtDNA heteroplasmy, as an indicator of cellular metabolic dysfunction, in turn leads to elevated metabolic abnormality due to amino acid coding change in key oxidative phosphorylation proteins. (northwestern.edu)

Ubiquitination is a multifunctional posttranslational modification controlling the activity, subcellular localization and stability of proteins. (cipsm.de)
Subcellular localization prediction of predicted BoGST proteins was performed using Protcomp 9.0 from Softberry [96]. (molquest.com)

Myristoylation is significant because a myristoyl group (fatty acid group) is added to the site which helps anchor the transmembrane protein or cytosolic protein to the membrane. (wikipedia.org)
Diabetes results in a cardiomyopathy characterized by decreased cardiomyocyte function, increased myocardial fatty acid utilization, decreased glucose utilization, increased myocardial oxygen consumption, and decreased cardiac efficiency ( 4 , 5 ), primarily as the result of changes in metabolism and Ca 2+ handling within the myocyte ( 3 , 6 , 7 ). (diabetesjournals.org)
However, little is known about the fatty acid transport mechanism in N. caninum . (biomedcentral.com)
This deletion did not affect the overall fatty acid composition but modified the abundance of TAG. (biomedcentral.com)
Before entering lipid synthesis pathways, different kinds of acyl-CoA transporters which acts as the major carrier of acyl-CoAs, such as fatty acid binding protein (FABP), sterol carrier protein 2 (SCP2) and acyl-CoA-binding protein (ACBP), would activate and convert fatty acids to fatty acyl-CoA esters via a reaction catalyzed by fatty acyl-CoA synthetase and transported to various metabolic locations [ 11 ]. (biomedcentral.com)

C11orf98 contains 4 bipartite nuclear localization signals (NLS_BP) which indicates the protein will be 'tagged' for import into the cell nucleus by nuclear transport. (wikipedia.org)

2020). RNA-Seq analysis of anthesis and post-anthesis periods in maize show different expression patterns of ZmHsf family members. (grassius.org)

During male gametogenesis, the proteins were also dispersed throughout the nucleus. (pberghei.eu)

The lipidomic analysis showed that disruption of NcACBP caused no obvious changes in the overall abundance and turnover of fatty acids while knockout resulted in the accumulation of triacylglycerol. (biomedcentral.com)

Lipid synthesis requires bulk carbon skeleton acyl-CoAs, the transport of which depends on the acyl-CoA binding protein (ACBP). (biomedcentral.com)
Fatty acids provide the acyl skeleton for lipid synthesis. (biomedcentral.com)

The spliceosome complex, composed of at least 170 proteins and several small nuclear RNAs (snRNAs), is the key structure responsible for splicing in eukaryotes 10 . (nature.com)
In plants, RNase III Dicer-like proteins (DCLs) act as sensors of dsRNAs and process them into short 21- to 24-nucleotide (nt) (s)RNAs. (biomedcentral.com)
Plant Dicer-like proteins (DCLs) are RNase III, double-stranded RNA (dsRNA)-specific endonucleases with specialized functions in producing short (s)RNAs of 21- to 24-nucleotides (nt), including micro (mi)RNAs and short interfering (si)RNAs of endogenous or viral origin. (biomedcentral.com)

Two protein-protein interaction sites on the spliceosome-associated human cyclophilin CypH. (nih.gov)

Removal of the H3K9me binding protein PaHP1 provided further support to the notion that each type of heterochromatin requires the presence of the other. (biomedcentral.com)
Here we identify Heterochromatin Protein 1β (HP1β) as an essential protein for proper differentiation, and, unexpectedly, for the maintenance of pluripotency in ESCs. (biomedcentral.com)

Modulating agents include human E3 ubiquitin ligases, antibodies thereto and variants thereof, as well as related proteins. (justia.com)
Activation and nuclear translocation of NF-κB occurs following signal-induced phosphorylation of IκB, which leads to proteolysis via the ubiquitin pathway. (justia.com)
Degradation of a protein via the ubiquitin pathway proceeds by two discrete and successive steps: (a) covalent attachment of multiple ubiquitin molecules to the protein substrate, and (b) degradation of the targeted protein by the 26S proteasome complex. (justia.com)

Gene therapy displacement of endogenous MCUb with a dominant-negative MCUb transgene (MCUb W246R/V251E ) in vivo rescued T2D cardiomyocytes from metabolic inflexibility and stimulated cardiac contractile function and adrenergic responsiveness by enhancing phospholamban phosphorylation via protein kinase A. We conclude that MCUb represents one newly discovered molecular effector at the interface of metabolism and cardiac function, and its repression improves the outcome of the chronically stressed diabetic heart. (diabetesjournals.org)

May 22, 2021 … The nucleus has a double membrane called nuclear envelope. (giibi.com)
Vaccinia Virus Protein C6 Inhibits Type I IFN Signalling in the Nucleus and Binds to the Transactivation Domain of STAT2 · Author Summary. (giibi.com)
In early schizonts within host red blood cells, we observed discrete foci in the parasite cell adjacent to the nuclear DNA for both SMC2 and SMC4, whereas in mature schizonts, the signal was dispersed throughout the nucleus. (pberghei.eu)

The secondary structures of the c11orf98 protein was predicted to have multiple alpha helices as well as beta sheets. (wikipedia.org)
The peptide transporter carbon starvation (CstA) family (transporter classification [TC] 2.A.114) belongs to the second largest superfamily of secondary transporters, the amino acid/polyamine/organocation (APC) superfamily. (cipsm.de)

The predicted molecular weight of the protein is 14.2 kDa. (wikipedia.org)

CcThi1 scavenges the required thiamine and thus arrests the thiamine sharing behavior of P. sojae from the supplier, which interferes with amino acid metabolism and expression of pathogenic effectors, probably leading to impairment of P. sojae growth and pathogenicity. (bvsalud.org)

Plant TRANSPARENT TESTA GLABRA (TTG) proteins regulate various developmental activities via the auxin signaling pathway. (biomedcentral.com)

Crystal structure of the human U4/U6 small nuclear ribonucleoprotein particle-specific SnuCyp-20, a nuclear cyclophilin. (nih.gov)

A variety of extracellular stimuli including mitogens, cytokines, antigens, stress inducing agents, UV light and viral proteins initiate a signal transduction pathway that ultimately leads to NF-κB release and activation. (justia.com)

The c11orf98 protein is expressed in a wide array of tissues. (wikipedia.org)

In contrast to the popular SRP model, RNA seq analysis in combination with qPCR and microscopic data revealed that mRNAs coding for nuclear-related proteins can also localize to ER. (uni-tuebingen.de)

It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. (nature.com)

Nonetheless, the association signal primarily arises from de novo protein-truncating variants, as opposed to the more common missense variants. (springer.com)
The evidence, however, largely comes from protein-truncating variants (PTVs) as opposed to de novo missense (dnMis) variants. (springer.com)
For the ASC study, only the most damaging class of dnMis variants-as judged by a composite score involving evolutionary conservation and likelihood an amino acid substitution is damaging [ 6 ]-shows strong signal for enrichment in ASD subjects. (springer.com)

Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)

In this study, we identify a previously uncharacterised isoform of microtubule-associated protein MAP4, oMAP4, as a microtubule organising factor that is crucial for myogenesis. (elifesciences.org)
Compositions and methods for modulating the activation of nuclear factor κB (NF-κB) are provided. (justia.com)
The present invention relates generally to compositions and methods for modulating the activation of nuclear factor κB (NF-κB). (justia.com)

The process starts from extracted genomic DNA, which contains both mtDNA and nuclear DNA, without the need to purify mitochondria. (northwestern.edu)
Total genomic DNA is the starting material for mtDNA-seq. (northwestern.edu)

I propose that that Mrn1p, Whi3p, Pbp2p, Slf1p, and Ngr1p are involved in controlling the expression of nuclear-encoded MRPs. (uni-tuebingen.de)

A family of microtubule-associated proteins (or 'MAPs' for short) bind to microtubules and assist in organising the filaments, but it is not clear how they work. (elifesciences.org)

PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. (springer.com)

Oomycete pathogens secrete numerous crinkling and necrosis proteins (CRNs) to manipulate plant immune and promote infection. (bvsalud.org)

C11orf98 is a protein-encoding gene on chromosome 11 in humans of unknown function. (wikipedia.org)

While there are numerous NUMTs existing in the nuclear DNA, the primers we use for mtDNA enrichment is highly specific to avoid any potential amplification of NUMTs from nuclear DNA. (northwestern.edu)

At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. (stanford.edu)

Nuclear extract, of the indicated cell lines, were separated on a 10% gel using SDS-PAGE, transferred to a PDF membrane and Western blotted using standard protocols. (encodeproject.org)
Roquin proteins preclude spontaneous T cell activation and aberrant differentiation of T follicular helper (Tfh) or T helper 17 (Th17) cells. (cipsm.de)
Cell 75:495, 1993), and a series of unique E6-AP homologous proteins have been identified (Huibregtse et al. (justia.com)
TotalSeq™ reagents are designed to profile protein levels at a single cell level following an optimized protocol similar to the CITE-seq workflow. (biolegend.com)

PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)

NUSeq provides mtDNA-seq for detection of specific mtDNA mutations associated with a disease, determination of mtDNA heteroplasmy, and haplogroup classification (Fig. 2). (northwestern.edu)

For ASH1 E3 LE recognition by She2p/She3p, the she2p tetramer uses two identical sets of amino acids (N36, R43, R52, K60, and R63) to contact RNA, while its protruding helix seems to be important for interaction with She3p. (uni-tuebingen.de)
In S. cerevisiae , this interaction is at least in part provided by Spp1 that directly interacts with both methylated H3K4 near DSB sites and the axis-localized protein Mer2 (Acquaviva et al. (springer.com)

The GLUT2 facilitated glucose transporter isoform is a membrane protein present in the pancreatic .beta. (justia.com)

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