Tag: ncRNA

2.1. Specificity SnoRNAs are ubiquitous and highly abundant RNAs [21,28]. So, how can one target the malignant cell with little to no harm to healthy cells? Recent publications have demonstrated that some rRNA modifications occur in sub-stoichiometric levels [10,29]. This finding has overturned the notion that all rRNA modifications are…

Behavioral testing After undergoing a four-day training program, the mice were subjected to a positioning cruise experiment on the fifth day. The experiment involved comparing the escape latency and swimming distance in the quadrant opposite to the platform between the WD group and the control group. The findings indicated that…

Non-Coding RNA 2023, 9(3), 34; doi.org/10.3390/ncrna9030034 (registering DOI) Non-Coding RNA 2023, 9(3), 34; doi.org/10.3390/ncrna9030034 (registering DOI) Received: 29 April 2023 / Revised: 26 May 2023 / Accepted: 2 June 2023 / Published: 7 June 2023 Round 1 Reviewer 1 Report I would elaborate more on miR-451 for two reasons, 1) it is…

Review . 2023 May 18;14:1123448. doi: 10.3389/fmicb.2023.1123448. eCollection 2023. Affiliations Expand Affiliation 1 School of Life Sciences, Jiangsu University, Zhenjiang, China. Item in Clipboard Review Yi-Xuan Fan et al. Front Microbiol. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 May 18;14:1123448. doi: 10.3389/fmicb.2023.1123448. eCollection 2023. Affiliation 1 School…

1. Introduction In recent years, growing access to massive transcriptome sequencing technologies has led to the discovery of an increasing number of novel transcripts from various species. The majority of these transcripts result in non-coding ribonucleic acid (ncRNA) molecules, short sequences of RNA that, with the exception of a small…

Introduction Escherichia coli, a member of the Enterobacterales family, is a common opportunistic pathogen that can cause various infectious illnesses, including urinary tract infections (UTIs) and other infections acquired in the community.1,2 The presence of carbapenemases in E. coli poses a serious threat to public health. These carbapenemase genes may…

Database, 2016, 1 doi: 10.1093/database/baw053 Erratum Erratum Ensembl comparative genomics resources Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon , Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha, Andrew Yates and Paul Flicek doi:10.1093/database/bav096 ncRNA orthologies in the vertebrate…

Introduction Although globalization has provided opportunities for consumers to enjoy a wide range of products and expanded global food trade, the complexity of the international food supply has contributed to an increase in foodborne outbreaks (Quested et al., 2010; Hussain and Dawson, 2013). Worldwide efforts have ensured food safety by…

Entry 220202            CDS       T01001                                  Symbol ATOH7, Math5, NCRNA, PHPVAR, RNANC, bHLHa13 Name (RefSeq) atonal bHLH transcription factor 7   KO K09083   atonal protein 1/7 Organism hsa  Homo sapiens (human) Disease H02112   Persistent hyperplastic primary vitreous Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03000 Transcription factors [BR:hsa03000]    220202 (ATOH7)Transcription factors [BR:hsa03000] Eukaryotic type  Basic…

Non-coding RNA (ncRNA) classes take over important housekeeping and regulatory functions and are quite heterogeneous in terms of length, sequence conservation and secondary structure. High-throughput sequencing reveals that the expressed novel ncRNAs and their classification are important to understand cell regulation and identify potential diagnostic and therapeutic biomarkers. To improve…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::11/29/2018 17:00:26 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.7 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,547 CDSs (total)::3,497 Genes (coding)::3,340 CDSs (with protein)::3,340 Genes (RNA)::50 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S,…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::07/05/2018 17:04:05 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.5 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,756 CDS (total)::5,710 Genes (coding)::5,642 CDS (coding)::5,642 Genes (RNA)::46 rRNAs::2, 4, 1 (5S, 16S, 23S) complete rRNAs::2, 1, 1 (5S, 16S,…

# Total IDs searched 9,648,246 IDs being used by LitScan 8,939,826 Unique RNA sequences 4,497,573 Articles found 865,179 RNAcentral LitScan is a new text mining pipeline that connects RNA sequences with the latest open access scientific literature. LitScan uses a collection of identifiers (Ids), gene names, and synonyms provided to…

Abstract Non-coding RNAs (ncRNAs) are a class of RNA molecules that lack the ability to encode proteins in human cells, yet play crucial roles in various biological process. Understanding these relationships and how different ncRNAs interact with each other to affect diseases can vastly contribute to their diagnosis, prevention, and…

Received: 19 January 2023 / Revised: 2 May 2023 / Accepted: 16 May 2023 / Published: 19 May 2023 Round 1 Reviewer 1 Report Terrazan and coworkers presented the manuscript entitled “ Inverse impact of cancer drugs on circular and linear RNAs in 2 breast cancer cell lines ”. The…

Background. Calcific aortic valve disease (CAVD) is the most common native valve disease. Valvular interstitial cell (VIC) osteogenic differentiation and valvular endothelial cell (VEC) dysfunction are key steps in CAVD progression. Circular RNA (circRNAs) is involved in regulating osteogenic differentiation with mesenchymal cells and is associated with multiple disease progression,…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/23/2022 10:50:15 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,042 CDSs (total)::3,933 Genes (coding)::3,880 CDSs (with protein)::3,880 Genes (RNA)::109 rRNAs::11, 12, 9 (5S, 16S, 23S) complete rRNAs::6, 1, 1…

Non-Coding RNA 2023, 9(3), 31; doi.org/10.3390/ncrna9030031 (registering DOI) Non-Coding RNA 2023, 9(3), 31; doi.org/10.3390/ncrna9030031 (registering DOI) Received: 26 March 2023 / Revised: 8 May 2023 / Accepted: 9 May 2023 / Published: 15 May 2023 Round 1 Reviewer 1 Report Dear authors, I have read with interest your paper. I find it…

Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the “queen of the mushroom” for its attractive appearance. D. rubrovolvata has been widely cultivated in China in recent years, and many researchers were focusing on its nutrition, culture condition and artificial cultivation. Due to…

Transcribed image text: Which of the following are correct statements about noncoding RNAs? a. Cells can have many types of ncRNA genes that are transcribed and translated to produce snRNA, piRNAs, miRNA, and others. b. ncRNAs play role in DNA replication, chromatin structure, transcription, splicing, genome defense, RNA modification, and…

Noncoding RNAs (ncRNAs) play crucial roles in many cellular life activities by interacting with proteins. Identification of ncRNA-protein interactions (ncRPIs) is key to understanding the function of ncRNAs. Although a number of computational methods for predicting ncRPIs have been developed, the problem of predicting ncRPIs remains challenging. It has always…

Received: 27 March 2023 / Revised: 1 May 2023 / Accepted: 4 May 2023 / Published: 8 May 2023 Round 1 Reviewer 1 Report This manuscript by Distefano et al, aimed at investigating whether lncRNAs would be important as important elements for Type II diabetes (T2D). The authors used previous…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::12/27/2018 19:23:50 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.7 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,099 CDSs (total)::5,045 Genes (coding)::4,882 CDSs (with protein)::4,882 Genes (RNA)::54 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S,…

Allis CD, Jenuwein T. The molecular hallmarks of epigenetic control. Nat Rev Genet. 2016;17:487–500. Article  CAS  PubMed  Google Scholar  Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 2022;50:D231–D235. Article  CAS  PubMed  Google…

Mapping of ncRNA expression across mouse organs We sequenced 771 tissue samples of the TMS cohort to map molecular shifts across the whole organism during healthy aging (Fig. 1a). The protocol enriches for small ncRNA, especially mature miRNAs. Even though full-length reads cover only small ncRNAs (miRNAs or piwi-interacting RNAs…

Abstract Non-coding RNAs (ncRNAs) play a critical role in regulating gene expression during development and in the pathogenesis of diseases. In particular, microRNAs have been extensively studied in the context of neurogenesis, the differentiation of pain sensing nociceptive neurons and the pathogenesis of pain disorder, however, little is known about…

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of…

Ren J, Yan X, Ai H, Zhang Z, Huang X, Ouyang J, Yang M, Yang H, Han P, Zeng W, et al. Susceptibility towards enterotoxigenic Escherichia coli F4ac diarrhea is governed by the MUC13 gene in pigs. PLoS ONE. 2012;7(9):e44573. Article  CAS  PubMed  PubMed Central  Google Scholar  Guinée P, Jansen…

PRESS RELEASE Published April 21, 2023 New York, Non-coding RNA (ncRNA) is a type of RNA molecule that does not code for protein synthesis but plays a crucial role in the regulation of gene expression. These ncRNAs have emerged as promising therapeutic targets, biomarkers, and diagnostic tools for a wide…

Company Logo Global Ngs-Based Rna-Sequencing Market Global Ngs-Based Rna-Sequencing Market Dublin, April 18, 2023 (GLOBE NEWSWIRE) — The “NGS-Based RNA-Sequencing Global Market Report 2023” report has been added to ResearchAndMarkets.com‘s offering. This report provides strategists, marketers and senior management with the critical information they need to assess the market. The…

Introduction Gout is an inflammatory disease caused by the deposition of monosodium urate (MSU) crystals in joints and other non-joint tissues. The main clinical manifestations of gout include recurrent joint redness, swelling, heat and pain, and even joint mutilation, urinary acid nephropathy and renal failure.1,2 The incidence and prevalence of…

Report Description: The RNA Sequencing Services Market 2023 research report appears to cover various aspects of the market, including the strategies of top players, market segments, competitive landscape, manufacturing, and pricing structures.  In this report, we will provide an in-depth analysis of the current state of the global RNA Sequencing…

With the rapid development of next-generation sequencing technology, several studies have shown that ncRNAs can act as competitive endogenous RNAs (ceRNAs) and are involved in various biological processes, such as proliferation, differentiation, apoptosis, and migration of breast cancer (BC) cells, and plays an important role in BC progression as a…

Non-Coding RNA 2023, 9(2), 29; doi.org/10.3390/ncrna9020029 (registering DOI) Non-Coding RNA 2023, 9(2), 29; doi.org/10.3390/ncrna9020029 (registering DOI) Received: 6 March 2023 / Revised: 8 April 2023 / Accepted: 13 April 2023 / Published: 18 April 2023 Round 1 Reviewer 1 Report The main question of this study was to investigate if molecules mimicking…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::11/20/2015 18:41:21 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes::4,429 CDS::4,289 Pseudo Genes::51 rRNAs::7, 6, 6 (5S, 16S, 23S) complete rRNAs::7 (5S) partial rRNAs::6, 6 (16S, 23S) tRNAs::70 ncRNAs::0 ##Genome-Annotation-Data-END## Read…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/12/2020 16:04:36 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.12 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::6,023 CDSs (total)::5,968 Genes (coding)::5,473 CDSs (with protein)::5,473 Genes (RNA)::55 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. Note This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewer Open rRNA processing…

NCT04406831 Serum miRNAs Pancreatic cancer – Recruiting NCT04305366 miRNA signatures Squamous cell carcinoma of head and neck – Recruiting NCT04435756 miRNA 371 Germ cell tumors – Recruiting NCT03738319 miRNA signatures High-grade serous ovarian cancer – Unknown NCT03779022 miRNA biomarkers Breast cancer – Unknown NCT04972201 Liquid biopsy miRNA Multi-cancer – Recruiting…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/04/2022 11:23:08 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,440 CDSs (total)::4,351 Genes (coding)::4,331 CDSs (with protein)::4,331 Genes (RNA)::89 rRNAs::6, 7, 2 (5S, 16S, 23S) complete rRNAs::6, 7, 2…

Introduction Breast cancer is the second most common cancer and is the leading cause of cancer-related death among females worldwide with over 2 million newly diagnosed cases and more than 60 thousand deaths every year.Citation1 Despite advances in treatment, the mortality rate of breast cancer remains high, mainly due to…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/05/2022 11:08:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::6,035 CDSs (total)::5,966 Genes (coding)::5,796 CDSs (with protein)::5,796 Genes (RNA)::69 rRNAs::1, 3, 6 (5S, 16S, 23S) complete rRNAs::1 (5S) partial…

1. Introduction Long non-coding RNAs are identified as a type of non-coding RNA that is longer than 200 nucleotides, and which does not have the potential to be translated into protein. Long non-coding RNAs influence various cellular regulatory processes, including chromatin remodeling, RNA processing, transcriptional regulation, and translational control. Recent…

Sci-Hub | Small ncRNA binding protein, PIWI: A potential molecular bridge between Blood Brain Barrier and Neuropathological conditions. Medical Hypotheses, 109609 | 10.1016/j.mehy.2020.109609 ◂ ↓ save Roy, R., Pattnaik, S., Sivagurunathan, S., & Chidambaram, S. (2020). Small ncRNA binding protein, PIWI: A potential molecular bridge between Blood Brain Barrier and…

Comput Struct Biotechnol J. 2023; 21: 2276–2285. ,a,1 ,a,1 ,a ,b,c and a,b,⁎ Leiming Jiang aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Shijia Hao aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Lirui Lin aComputational…

Once considered unimportant “junk DNA,” scientists have learned that non-coding RNA (ncRNA) — RNA molecules that do not translate into proteins — play a crucial role in cellular function. Mutations in ncRNA are associated with a number of conditions, such as cancer, autism, and Alzheimer’s disease. Now, through the use…

1. Introduction Many studies have identified some non-coding RNAs (ncRNAs) with abnormal expressions in several diseases and/or disorders [1]. Among them, circular RNAs (circRNAs) are a special type of endogenous ncRNAs, probably formed by back-splicing events, which have attracted more and more interest nowadays. CircRNAs are closed loop structures [2],…

Match each description below at left with the correct molecular player involved in either transcription or translation from among the options in the drop-down menus at right (not all options will be used, but those that are will be used only once).1. binds to A site of ribosome during translation…

Mehari is a software package for annotating VCF files with variant effect/consequence. The program uses hgvs-rs for projecting genomic variants to transcripts and proteins and thus has high prediction quality. Other popular tools offering variant effect/consequence prediction include: Mehari offers predictions that aim to mirror VariantValidator, the gold standard for…

As we enter the third decade of the post-genomic era, the role of the non-coding parts of the human genome in diseases is becoming progressively better elucidated. An increasing number of lncRNAs have been recently linked to multiple pathogenesis mechanisms, including those underlying cancers, and developmental and metabolic disorders, as…

A bacterial ncRNA called OxyS binds to the Shine-Dalgarno ribosomal binding sequence, whichprevents ribosome binding. This is what type of gene regulation? Post-transcriptionalTranscriptional Translational Post-translationalThe ncRNA HOTAIR recruits histone-modifyingcomplexes and alters chromatin structure, and thereby represses transcription. This is which levelof gene regulation? Translational Post-transcriptional Transcriptional Post-translationalTranscriptional regulatory proteins recognize…

1. Introduction Cancer is one of the main causes of death around the world, with the most significant being lung, liver, stomach, colon, and breast cancers. As a major concern, the dissemination of metastases is responsible for more than 90% of deaths by cancer. Tumor cells spread by lymphatic and…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::11/03/2020 18:15:02 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.13 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,578 CDSs (total)::2,494 Genes (coding)::2,447 CDSs (with protein)::2,447 Genes (RNA)::84 rRNAs::7, 6, 6 (5S, 16S, 23S) complete rRNAs::7, 6, 6…

I searched for the id 85009 in ncbi gene website. I got results from gene summary with informations Gene type : ncRNA But, when I tried for the same in eutils the ouput did not contain this information. I want to perform this for multiple genes. esummary -db gene -id…

ReportLinker Major players in the ngs-based rna-sequencing market are Illumina, Thermo Fischer Scientific, Oxford Nanopore, Agilent Technologies Inc., BGI, PerkinElmer Inc., QIAGEN, Eurofins Scientific, F Hoffmann-La Roche Ltd. New York, March 21, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “NGS-Based RNA-Sequencing Global Market Report 2023” –…

How to calculate the Z value of infernal cmscan? 1 The infernal Userguide says(link) But the website of Rfam Help says(link) Which is correct？If the infernal Userguide is correct, the number of CMs is 4108, am I right? And I also want to know what would happen if I run…

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::05/11/2022 13:38:39 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,371 CDSs (total)::5,288 Genes (coding)::5,122 CDSs (with protein)::5,122 Genes (RNA)::83 rRNAs::6, 5, 5 (5S, 16S, 23S) complete rRNAs::6, 5,…

Non-Coding RNA 2023, 9(2), 20; doi.org/10.3390/ncrna9020020 (registering DOI) Non-Coding RNA 2023, 9(2), 20; doi.org/10.3390/ncrna9020020 (registering DOI) Received: 17 January 2023 / Revised: 24 February 2023 / Accepted: 13 March 2023 / Published: 17 March 2023 Round 1 Reviewer 1 Report Dear Authors, first of all congratulations for your interesting work and effort….

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::12/05/2018 18:00:42 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.7 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,796 CDSs (total)::4,745 Genes (coding)::4,671 CDSs (with protein)::4,671 Genes (RNA)::51 rRNAs::2, 1, 1 (5S, 16S, 23S) complete rRNAs::2, 1, 1 (5S,…

PRESS RELEASE Published March 15, 2023 The non-coding RNA assays market has been growing steadily in recent years, driven by the increasing demand for better understanding of non-coding RNA (ncRNA) molecules and their role in various biological processes. Non-coding RNAs are RNA molecules that do not code for proteins but…

Grammar String: a Novel ncRNA Secondary Structure Representation Rujira Achawanantakun, Seyedeh Shohreh Takyar, Yanni Sun* Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA. yannisun@cse.msu.edu Proc LSS Comput Syst Bioinform Conf. August, 2010. Vol. 9, p. 2-13. Full-Text PDF *To whom correspondence should be addressed….

Grabowski P, Zaug A, Cech T. The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena. Cell. 1981;23(2):467–76. Article  CAS  PubMed  Google Scholar  Ye C, Chen L, Liu C, Zhu Q, Fan L. Widespread noncoding circular RNAs in plants. New Phytol….

In molecular biology, Circular RNAs (circRNAs) refer to a class of circular RNA molecules found across all kingdoms of life.[1][2][3] Studies in 2013 have suggested that circRNAs play important regulatory roles in miRNA activity. Researchers found that CDR1as circRNA acts as a miR-7 super-sponge that contains about 70 target sites…

Received: 9 February 2023 / Revised: 4 March 2023 / Accepted: 6 March 2023 / Published: 9 March 2023 Round 1 Reviewer 1 Report In this paper, they reviewed the role of a long non-coding RNA, H19, in liver cancer. H19 is a lncRNA, which has been extensively studied. Multiple…

Here is the database with 3,898 ncRNA that was compared to the set of lncRNA indentified by us. The database was built based on the papers below: Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans -silencing of the Ty1 retrotransposon in S. cerevisiae. Genes…

Chan, K. S. et al. Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells. Proc. Natl Acad. Sci. USA 106, 14016–14021 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  Adams, S. et al. Signal-regulatory protein is selectively expressed by myeloid and neuronal cells. J. Immunol. 161,…

2. MicroRNA Biogenesis and Targeting MiRNAs are small non-coding single-stranded RNAs encoded within non-coding sequences of the genome; however, a minority of miRNAs are known to also be encoded within exons [3]. Interestingly, miRNAs located within intronic regions of protein-coding genes can be transcribed from the same promoter as a…

Non-Coding RNA 2023, 9(2), 17; doi.org/10.3390/ncrna9020017 (registering DOI) Non-Coding RNA 2023, 9(2), 17; doi.org/10.3390/ncrna9020017 (registering DOI) Received: 30 January 2023 / Revised: 21 February 2023 / Accepted: 21 February 2023 / Published: 28 February 2023 Round 1 Reviewer 1 Report In this manuscript, the authors analyze miRNA signatures in the partial remission…

How I Remove Ncrna From Raw Reads? 1 to remove ncRNA from raw reads I use Bowtie2 by making a ncRNA index. But after aligning with this index I want to save the reads those are showing no match with this index. how do I do that. I am using…

Problem Statement: This question asks to write a script to obtain all protein sequences coded in the human genome in the multiple FASTA format, using the RefSeq table obtained from the UCSC Table Browser and the human genome obtained from the given URL. The ID of each sequence should be…

Non-Coding RNA 2023, 9(1), 14; doi.org/10.3390/ncrna9010014 (registering DOI) Non-Coding RNA 2023, 9(1), 14; doi.org/10.3390/ncrna9010014 (registering DOI) Received: 8 December 2022 / Revised: 31 January 2023 / Accepted: 9 February 2023 / Published: 11 February 2023 Round 1 Reviewer 1 Report The authors present a novel mechanism by which MALAT1 promotes EMT in…

Non-coding RNA (ncRNA) is a special type of RNA transcript that makes up more than 90 % of the human genome. Although ncRNA typically does not encode proteins, it indirectly controls a wide range of biological processes, including cellular metabolism, development, proliferation, transcription, and post-transcriptional modification. NcRNAs include small interfering…

How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file. 2 I have recently annotated a genome using mikado. However, the resultant gff file contains loci that are overlapping but not annotated as isoforms: i.e. chr17 Mikado_loci ncRNA_gene 1014098 1014976 17 – . ID=Fly1;Name=Fly1;multiexonic=True;superlocus=Mikado_superlocus:chr17-:1014059-1015028 chr17…

ncRNA-mRNA interaction prediction 0 Hi everyone, Could someome give me recommendations of methodologies to predict ncRNA-mRNA interactions between species? I’m interested in using this information to study host-parasite interaction. The only way I can think now is by base-pairing approach. Thanks! ncRNAs interspecies interaction • 26 views • link 3…

By applying the proposed methodology of our study, we conducted the last search on 14 February 2022 on all three platforms, yielding 272 articles, of which 102 duplicates were excluded through Zotero 6.0. (Corporation for Digital Scholarship, 2022). Two authors independently read the remaining 170 articles. After reading the abstracts,…

The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL)…

Επιτομή The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial…

Received: 14 January 2023 / Revised: 28 January 2023 / Accepted: 30 January 2023 / Published: 31 January 2023 Round 1 Reviewer 1 Report This review manuscript aims at providing comprehensive information on linc-ROR in different pathological conditions. The number of publications considered is huge and the authors make a…

A variety of research technologies that make use of exogenous non-coding RNAs (ncRNAs) are used in cell biology research. These involve the introduction of specific types of ncRNA in order to manipulate an aspect of the recipient cell. In each case, the ability to target a specific endogenous nucleic acid…

doi: 10.3389/fonc.2022.1025192. eCollection 2022. Affiliations Expand Affiliations 1 Department of Oncology, Wuhan Third Hospital, Wuhan, Hubei, China. 2 North Sichuan Medical College, Nanchong, Sichuan, China. 3 Department of Thoracic Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China. 4 Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of…

Review . 2022 Nov;16(16):1181-1191. doi: 10.2217/bmm-2022-0349. Epub 2023 Jan 23. Affiliations Expand Affiliations 1 Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People’s Republic of China. 2 Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, People’s Republic of China. Item…

A recent catalogue of human transcriptome, namely CHESS database, assembled from RNA sequencing experiments as a part of the Genotype-Tissue Expression (GTEx) Project reported more non-coding RNA genes (21,856) than protein-coding (21,306), revealing an unexpectedly vast amount of transcriptional noise (Pertea et al, 2018). In this study, we introduce…

This unit briefly describes the two fundamentally different methods for predicting RNA structures. The first is to find that structure with the minimum free energy of folding, as predicted by various thermodynamic parameters related to base-pair stacking, loop lengths, and other features. If one has only a single sequence,…

ncRNA-seq Results Explained: What you can explore with non-coding RNA data Non-coding RNA-sequencing (ncRNA-seq) is a powerful technique for studying the regulatory functions of different types of ncRNAs in gene expression: from long non-coding RNA sequencing (lncRNA-seq), small RNA sequencing (sRNA-seq) to circular RNA sequencing (circRNA-seq) for diverse eukaryotic species….

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

Javascript is currently disabled or is not supported by this browser. Please enable JavaScript for full functionality. Sorry, there was a problem loading sequence from server. Please try again and contact us if the problem persists. Automated summary: This ncRNA sequence is 53 nucleotides long and is found in Candidatus…

Objective biomarkers for the fatal neurodegenerative disease amyotrophic lateral sclerosis or motor neuron disease (ALS/MND) are critical for diagnosis, drug development, clinical trials, and insight into disease pathology. Key candidates for biomarkers present in biofluids include non-coding RNA (ncRNA) transcripts including microRNA, piwi-interacting RNA and transfer RNA. To determine if…

It is generally considered that non-coding RNAs do not encode proteins; however, more recently, studies have shown that lncRNAs and circRNAs have ORFs which are regions that code for peptides/protein. On account of the lack of 5’cap structure, translation of circRNAs is driven by IRESs, m6A modification or through rolling…

doi: 10.3389/fgene.2022.958641. eCollection 2022. Affiliations Expand Affiliations 1 Laboratório de Ecofisiologia e Bioquímica de Plantas, Núcleo de Conservação da Biodiversidade, Instituto de Pesquisas Ambientais, São Paulo, SP, Brasil. 2 Programa de Pós-Graduação em Biologia Celular e Estrutural, Universidade Estadual de Campinas, Campinas, SP, Brasil. Item in Clipboard Camilla Alves Santos et…

Dear Colleagues, In recent decades, ncRNAs have been shown to play a critical role in a myriad of cellular processes, impacting normal gene expression as well as disease progression, making them an attractive target for drug discovery. Moreover, their complex impacts on molecular biology still require revealing and studying. Recent…

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

Non-Coding RNA 2022, 8(4), 56; doi.org/10.3390/ncrna8040056 (registering DOI) Non-Coding RNA 2022, 8(4), 56; doi.org/10.3390/ncrna8040056 (registering DOI) Received: 11 July 2022 / Revised: 18 July 2022 / Accepted: 19 July 2022 / Published: 22 July 2022 Round 1 Reviewer 1 Report Review on the manuscript titled “LiverDB: Systematic analysis of long non–coding RNA…

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of…

lncRNA analysis tutorial 2 hello, I would like to ask if there is some good tutorial concerning analysis of lncRNA along RNAseq analysis? like practical example. thank you for your help. lncRNA RNA-seq • 458 views Generally speaking, doing differential expression (DE) or transcript discovery on lncRNA is no different…

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq 0 Hi all, I have some small RNA-seq libraries from some plants. I downloaded ncRNA from Ensemble Plants as I don’t know how to use the Rfam database. How could I extract the rRNA/tRNA and other ncRNA ratios…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/29/2015 14:17:23 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes::4,587 CDS::4,486 Pseudo Genes::46 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S, 23S) partial rRNAs:: tRNAs::51 ncRNA::1 ##Genome-Annotation-Data-END##…

As shown in Figure 2A, LINC00892 is strongly induced in Jurkat cells following treatment with a combination of PMA and ionomycin. The reason for the concomitant use of PMA and ionomycin to induce T cell activation is based on the need to activate multiple signal transduction pathways. PMA is a…

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

Circular RNAs (circRNAs) are a novel class of regulatory RNA involved in many biological, physiological and pathological processes by functioning as a molecular sponge, transcriptional/epigenetic/splicing regulator, modulator of protein–protein interactions, and a template for encoding proteins. Cells are constantly dealing with stimuli from the microenvironment, and proper responses rely on…

Long non-coding RNAs (lncRNAs) are a class of RNAs that do not code for proteins and are typically greater than 200 nucleotides in length. Studies have shown that lncRNAs are quite complex in function and play an important role in various biological processes such as development, differentiation, proliferation, metastasis, apoptosis,…