Tag: utr

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Received: 1 March 2022 / Revised: 21 March 2022 / Accepted: 25 March 2022 / Published: 28 March 2022 Round 1 Reviewer 1 Report In recent years, a great process has been made in the research…

Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS  PubMed  PubMed Central  Google Scholar  Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…

Today I share a preprint article Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutic uploaded by Rhiju Das on BioRxiv , to explore the universal rules for achieving mRNA stability and efficient expression. Barriers to mRNA therapeutics With rapid R&D capabilities and extensive R&D pipelines, especially in…

Datasets and populations We first compiled whole-genome sequencing data to analyze the patterns of variation in ZTGs on two geographical levels. Thus, we explored a worldwide dataset of 2,328 unrelated individuals representing 24 populations across Africa (AFR), Europe (EUR), East Asia (EAS), South Asia (SAS) and America (AMR), denoted as…

. 2022 Mar 3;220(3):iyac017. doi: 10.1093/genetics/iyac017. Affiliations Expand Affiliations 1 Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA. 2 Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA. Item in Clipboard Hope M Healey et al. Genetics. 2022. Show details Display options Display options…

TargetScanHuman 7.1 * broadly conserved = conserved across most vertebrates, usually to zebrafish  conserved = conserved across most mammals, but usually not beyond placental mammals TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each…

Mobility of eukaryotic transposable elements (TEs) are finely regulated to avoid an excessive mutational load caused by their movement. The transposition of retrotransposons is usually regulated through the interaction of host- and TE-encoded proteins, with non-coding regions (LTR and 5′-UTR) of the transposon. Examples of new potent cis-acting sequences, identified…

Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…

QuantSeq 3’ mRNA-Seq Library Prep kits from Lexogen offers cost-efficient analysis of differential gene expression via 3’ mRNA-seq library preparation. Requiring fewer reads per samples and capable of multiplexing a high number of samples on a single sequencing lane, the 3’ mRNA-Seq technology simplifies your gene expression projects with no…

There are four types of methods to extract longest transcript or longest CDS regeion with longest transcript from transcripts fasta file or GTF file. 1.Extract longest transcript from gencode transcripts fasta file. 2.Extract longest transcript from gtf format annotation file based on gencode/ensembl/ucsc database. 3.Extract longest CDS regeion with longest…

Significance Tools that afford spatiotemporal control of gene expression are crucial for studying genes and processes in multicellular organisms. Stop cassettes consist of exogenous sequences that interrupt gene expression and flanking site-specific recombinase sites to allow for tissue-specific excision and restoration of function by expression of the cognate recombinase. We…

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

Fig. 1: miR-675 targets the DUX4 ORF and 3′UTR. a RenLuc-DUX4-FL dual-luciferase reporter and CMV.H19 constructs, and U6.MIR675, H1.MIR675, U6.MIR675-3p, and U6.MIR675-5p miRNAs. RenLuc-DUX4-FL contains DUX4 ORF and 3′UTR sequences fused to Renilla luciferase after the stop codon. Exons 1–3 are indicated (Ex1,2,3). *SD5 indicates silent mutation of a cryptic…

CONC 2006 SVM Eukaryotes (both protein-coding and non-coding genes) peptide length, amino acid composition, predicted secondary structure content, mean hydrophobicity, percentage of residues exposed to solvent, sequence compositional entropy, number of homologues, alignment entropy 10-fold CV on protein-coding: F1-score: 97.4% ☼ Precision: 97.1% ☼ Recall: 97.8% ◙ On non-coding: F1-score:…

A recent review in the Chemical and Pharmaceutical Bulletin looks at the molecular design of pH-sensitive cationic lipids and their applications for various tissues and cell types. The researchers also describe the application of lipid nanoparticles (LNPs) for delivering various macromolecules including small interfering ribonucleic acid (siRNA), antisense oligonucleotide, messenger…

Easy Way To Get 3′ Utr Lengths Of A List Of Genes 4 Hi, as the title says really, I’m wondering if there is any tool available that would allow me to drop in a list of say entrez gene ids and get their corresponding 3′ UTR lenghts? Thanks for…

Doubts with Stacked barplot using R ggplot2 0 Hello! I am trying to plot some data using R but I am having some problems doing it. I have a data frame with two columns (genes and and type of mutation) and looks like: genes variant MLH1 Intronic ATR 5′ UTR…

Calculate the fraction of genome that is feature X 2 I am trying to calculate enrichment of Structural variant breakpoints and SNV locations in genomic features (exon, intron, 5’UTR…) in a non-human genome. To know whether a feature is over/underrepresented in a SV/SNV dataset, I first need to know the…

DAPARS2 generate region annotation output bed’s size is 0 0 hello everyone, I want to generate region annotation using dapars2, but the output bed file’s size is zero, the bed file from the test data provided by dapars2 is also zero, the same as my data’s . Total extracted 3’…

How to trim a GFF3 file based on specific coordinates? 0 Hi, I would like to create a GFF3 file containing information only for specific coordinates from the chromosome level GFF3 file. I know how to extract gene and CDS info separately but don’t know how to do trimming based…

Hello, I am doing an experiment and I need to build a BED12 file for some UTR sequences that I have. I have done a blast for those sequences and with that I was able to build a successful BED6 file, like this: 19 20752377 20758767 ENSDARG00000062634_Kat2b_Tscan 0 + 15…