Tag: ncRNA

extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq

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…

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Root70 – Genome – Assembly

##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##…

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ncRNA | Free Full-Text | LINC00892 Is an lncRNA Induced by T Cell Activation and Expressed by Follicular Lymphoma-Resident T Helper Cells

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…

Continue Reading ncRNA | Free Full-Text | LINC00892 Is an lncRNA Induced by T Cell Activation and Expressed by Follicular Lymphoma-Resident T Helper Cells

Roles of circRNAs | CMAR

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…

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ncRNA | Free Full-Text | The Functional Roles and Regulation of Circular RNAs during Cellular Stresses

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…

Continue Reading ncRNA | Free Full-Text | The Functional Roles and Regulation of Circular RNAs during Cellular Stresses

LncRNA Sequencing Helps to Find Deep Links to Disease

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,…

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Environmental Factor – May 2022: Scientific moonshot: Now is the time to sequence RNA, expert says

Rick Woychik, Ph.D., directs NIEHS and the National Toxicology Program. (Image courtesy of NIEHS) Almost two decades have passed since the first sequence of a complete set of DNA was released as part of the Human Genome Project. That initiative expanded understanding of certain cancers, boosted the effectiveness of some…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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PDT001259745.1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Date::03/08/2022 21:07:51 Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Provider::NCBI Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Annotation Software revision::2021-01-11.build5132 Genes (total)::5,850 CDSs (total)::5,754 Genes (coding)::5,653 CDSs (with protein)::5,653 Genes (RNA)::96 rRNAs::4, 2, 3 (5S, 16S, 23S) complete rRNAs::4 (5S) partial…

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14 Postdoctoral Fellowship at Umea University, Sweden

Umea University, Sweden invites online Application for various Postdoctoral Fellowship in their different Departments. We are providing a list of Postdoc Fellowship positions available at Umea University, Sweden. Eligible candidate may Apply as soon as possible.   (01) Postdoctoral Fellowship Position Postdoc Fellowship Position summary/title: Postdoctoral fellow – Molecular epidemiology…

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ncRNA | June 2022 – Browse Articles

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…

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ASM1860456v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/02/2021 10:26:31 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,541 CDSs (total)::3,440 Genes (coding)::3,416 CDSs (with protein)::3,416 Genes (RNA)::101 rRNAs::9, 9, 9 (5S, 16S, 23S) complete rRNAs::9, 9,…

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LncRNA PCAT1 activates SOX2 and suppresses radioimmune responses via regulating cGAS/STING signalling in non-small cell lung cancer

This article was originally published here Clin Transl Med. 2022 Apr;12(4):e792. doi: 10.1002/ctm2.792. ABSTRACT BACKGROUND: The expression of long non-coding RNA (lncRNA) prostate cancer-associated ncRNA transcripts 1 (PCAT1) is increased in non-small cell lung cancer (NSCLC). It stimulates tumour growth and metastasis, but its role in the radioimmune responses remain…

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ASM1917534v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::08/30/2021 23:22:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,122 CDSs (total)::3,071 Genes (coding)::2,904 CDSs (with protein)::2,904 Genes (RNA)::51 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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Cardior Appoints Dr. Russell Greig as Independent Chairman of the Board

HANOVER, Germany–(BUSINESS WIRE)–Cardior Pharmaceuticals, a clinical-stage biotech company developing non-coding RNA (ncRNA)-based therapeutics for patients with cardiac diseases, today announced the appointment of Dr. Russell Greig, as independent Chairman of its Board of Directors. Dr. Greig brings more than 35 years of experience in the pharmaceutical industry from GlaxoSmithKline, with…

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ASM1863403v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/03/2021 14:29:20 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,407 CDSs (total)::4,307 Genes (coding)::4,183 CDSs (with protein)::4,183 Genes (RNA)::100 rRNAs::8, 7, 7 (5S, 16S, 23S) complete rRNAs::8, 7,…

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SAWRPI: A Stacking Ensemble Framework With Adaptive Weight for Predicting ncRNA-Protein Interactions Using Sequence Information

doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations Expand Affiliations 1 School of Information Engineering, Xijing University, Xi’an, China. 2 School of Computer Science, Northwestern Polytechnical University, Xi’an, China. Item in Clipboard Zhong-Hao Ren et al. Front Genet. 2022. Show details Display options Display options Format AbstractPubMedPMID doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations 1 School…

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ASM1814142v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::05/07/2021 12:52:22 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,858 CDSs (total)::4,780 Genes (coding)::4,742 CDSs (with protein)::4,742 Genes (RNA)::78 rRNAs::6, 6, 5 (5S, 16S, 23S) complete rRNAs::6, 6,…

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ncRNA | Free Full-Text | Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

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…

Continue Reading ncRNA | Free Full-Text | Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

ASM1922276v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::07/15/2021 15:46:43 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::8,257 CDSs (total)::8,191 Genes (coding)::8,106 CDSs (with protein)::8,106 Genes (RNA)::66 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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python beginner – faster way to find and replace in large file?

You should split your lines into “words” and only look up these words in your dictionary: >>> re.findall(r”\w+”, “CHROMOSOME_IV ncRNA gene 5723085 5723105 . – . ID=Gene:WBGene00045518 CHROMOSOME_IV ncRNA ncRNA 5723085 5723105 . – . Parent=Gene:WBGene00045518”) [‘CHROMOSOME_IV’, ‘ncRNA’, ‘gene’, ‘5723085’, ‘5723105’, ‘ID’, ‘Gene’, ‘WBGene00045518’, ‘CHROMOSOME_IV’, ‘ncRNA’, ‘ncRNA’, ‘5723085’, ‘5723105’, ‘Parent’,…

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ASM2099102v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::11/28/2021 12:10:22 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)::3,454 CDSs (total)::3,291 Genes (coding)::3,252 CDSs (with protein)::3,252 Genes (RNA)::163 rRNAs::14, 13, 13 (5S, 16S, 23S) complete rRNAs::14, 13,…

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The fitness tradeoff in LP promastigotes correlates with snoRNA expression changes and increased rRNA pseudouridinylation levels.

(A) Genomic map of L. donovani Ld1S ncRNA genes. (B) Composition of the small RNome identified in EP parasites. (C) Northern blot analysis of selected snoRNAs, Ld14Cs1H3 was used as loading control. Two representative northern blots out of four are presented. The analyses were performed with two independent cultures derived…

Continue Reading The fitness tradeoff in LP promastigotes correlates with snoRNA expression changes and increased rRNA pseudouridinylation levels.

ASM1890591v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::12/19/2021 14:49:10 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)::2,956 CDSs (total)::2,892 Genes (coding)::2,846 CDSs (with protein)::2,846 Genes (RNA)::64 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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ncRNA | Free Full-Text | Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes

The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, namely ribosome-associated non-coding RNAs (rancRNAs), has been…

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Understanding signatures of positive natural selection in human zinc transporter genes

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…

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ASM1993088v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::09/24/2021 10:50:11 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)::4,022 CDSs (total)::3,966 Genes (coding)::3,901 CDSs (with protein)::3,901 Genes (RNA)::56 rRNAs::3, 3, 3 (5S, 16S, 23S) complete rRNAs::3, 3,…

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GPP Web Portal – Transcript Details

Transcript: Human XR_933717.2 PREDICTED: Homo sapiens uncharacterized LOC105371334 (LOC105371334), ncRNA. Source: NCBI, updated 2019-09-08 Taxon: Homo sapiens (human) Gene: LOC105371334 (105371334) Length: 321 CDS: (non-coding) sgRNA constructs matching this transcript (CRISPRko, NGG PAM) This list includes CRISPRko constructs with 100% (20mer + NGG) sequence match to the exonic sequence of…

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RefSeq: XP_007190711

LOCUS XP_007190711 296 aa linear MAM 12-FEB-2019 DEFINITION reticulon-4-interacting protein 1, mitochondrial isoform X3 [Balaenoptera acutorostrata scammoni]. ACCESSION XP_007190711 VERSION XP_007190711.1 DBLINK BioProject: PRJNA237330 DBSOURCE REFSEQ: accession XM_007190649.2 KEYWORDS RefSeq. SOURCE Balaenoptera acutorostrata scammoni ORGANISM Balaenoptera acutorostrata scammoni Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea;…

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ASM2054021v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/15/2021 18:22:15 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)::4,439 CDSs (total)::4,349 Genes (coding)::4,268 CDSs (with protein)::4,268 Genes (RNA)::90 rRNAs::8, 2, 2 (5S, 16S, 23S) complete rRNAs::8 (5S) partial…

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ASM1736881v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::03/11/2021 17:21:49 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,842 CDSs (total)::2,777 Genes (coding)::2,722 CDSs (with protein)::2,722 Genes (RNA)::65 rRNAs::1, 1 (5S, 16S) complete rRNAs::1 (5S) partial rRNAs::1 (16S)…

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WikiHr > RefSeq

Database containing reference sequences of genes, proteins and transcripts The Reference Sequence (RefSeq) database[1] is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. RefSeq was first introduced in 2000.[2][3] This database is built by National Center for Biotechnology Information (NCBI),…

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Technological Advances in RNA Stabilization & Delivery

RNA therapeutics is a rapidly expanding field of next-generation medicine. RNA therapy typically comprises 4 different classes of molecules: non-codingRNA (ncRNA), antisense oligonucleotide (ASO), messengerRNA (mRNA), and RNA aptamer. New York, Jan. 27, 2022 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Technological Advances in RNA Stabilization &…

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ASM1584570v1 – Genome – Assembly

##Genome-Annotation-Data-START##Annotation Date::05/22/2015 10:24:41Annotation Method::Best-placed reference protein set; GeneMarkS+Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Provider::NCBIFeatures Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionAnnotation Software revision::2.10 (rev. 463717)Genes::5,665CDS::5,280Pseudo Genes::271CRISPR Arrays::4rRNAs::32 (5S, 16S, 23S)tRNAs::82ncRNA::1Frameshifted Genes::68##Genome-Annotation-Data-END## Read more here: Source link

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RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

Abstract Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However,…

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ncRNA | February 2022 – Browse Articles

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…

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What is RNAcentral? | RNAcentral

RNAcentral is a database of non-coding RNA sequences that aggregates ncRNA data from over 40 member resources known as Expert Databases.1 Non-coding RNAs Similar to mRNAs, non-coding RNAs (ncRNAs) are transcribed from DNA but are not translated into proteins. NcRNAs are found in all organisms and have a broad range…

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Detail

Detail Basic Information MNDR ID: Confidence Score: 0 ncRNA Information: …

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slobentanzer/ncrna-stroke – githubmemory

THIS IS THE BARE BONES VERSION OF Feeling Responsive All unnecessary files (images, posts) miss in this release to give you a quick and fresh start. If you are new to Feeling Responsive try the GH-Pages-Version. It teaches you with lots of material how to use this flexible theme. A…

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Graph clustering as a method to investigate riboswitch variation

Abstract Non-coding RNA (ncRNA) perform vital functions in cells, but the impact of diversity across structure and function of homologous motifs has yet to be fully investigated. One reason for this is that the standard phylogenetic analysis used to address these questions in proteins cannot easily be applied to ncRNA…

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ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

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:…

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Using STAR SJ.out.tab file to identify novel ncRNAs

Using STAR SJ.out.tab file to identify novel ncRNAs 0 Hi All, I am attempting to identify novel ncRNAs from a circadian RNAseq dataset. Specifically I have a ribo-depleted RNAseq timecourse with 31 samples (sample every 2 hours for 60hrs). I have run STAR (code below). I am trying to follow…

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ASM648341v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/22/2018 18:06:09 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::7,178 CDS (total)::7,112 Genes (coding)::6,886 CDS (coding)::6,886 Genes (RNA)::66 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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ASM296653v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::03/19/2021 18:16:01 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.1 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,877 CDSs (total)::1,821 Genes (coding)::1,767 CDSs (with protein)::1,767 Genes (RNA)::56 rRNAs::2, 2, 2 (5S, 16S, 23S) complete rRNAs::2, 2,…

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Research Fellow, Precision Medicine job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The NUS Resilience & Growth Research Fellow (NUS R&G-RF) will be responsible to work closely with the Principal Investigator and study team members to ensure the successful completion of industry-linked non-coding RNA (ncRNA) biomarker discovery research projects and subsequent functional validation of the identified ncRNA biomarkers in a…

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ASM350094v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/27/2018 21:42:42 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)::3,542 CDS (total)::3,498 Genes (coding)::3,451 CDS (coding)::3,451 Genes (RNA)::44 tRNAs::40 ncRNAs::4 Pseudo Genes (total)::47 Pseudo Genes (ambiguous residues)::2 of 47 Pseudo…

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ASM314399v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/15/2018 16:18:51 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)::1,893 CDS (total)::1,839 Genes (coding)::1,782 CDS (coding)::1,782 Genes (RNA)::54 rRNAs::3, 1, 1 (5S, 16S, 23S) complete rRNAs::3, 1 (5S, 16S) partial…

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ASM1227490v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::02/09/2021 05:00:21 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,608 CDSs (total)::4,469 Genes (coding)::4,408 CDSs (with protein)::4,408 Genes (RNA)::139 rRNAs::10, 9, 9 (5S, 16S, 23S) complete rRNAs::10, 9,…

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ASM298219v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::01/12/2021 08:24:12 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.0 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,192 CDSs (total)::5,077 Genes (coding)::4,870 CDSs (with protein)::4,870 Genes (RNA)::115 rRNAs::9, 8, 8 (5S, 16S, 23S) complete rRNAs::9, 8,…

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ASM212806v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/12/2020 21:58:49 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)::767 CDSs (total)::724 Genes (coding)::684 CDSs (with protein)::684 Genes (RNA)::43 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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ASM238634v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::06/05/2020 15:45:56 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::1,994 CDSs (total)::1,917 Genes (coding)::1,885 CDSs (with protein)::1,885 Genes (RNA)::77 rRNAs::4, 4, 4 (5S, 16S, 23S) complete rRNAs::4, 4,…

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RNAcentral Bioinformatician job with EMBL

RNAcentral is a leading database for non-coding RNA sequences. This resource is visited by tens of thousands of users every year, is highly cited and is currently funded by a Wellcome grant. RNAcentral is part of the Sequence Families group, which is led by Alex Bateman. You will be working…

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New Class of Transposon-Encoded RNA-Guided Nucleases May Add to Genome Editing Toolbox

NEW YORK – A team of US researchers led by the Broad Institute’s Feng Zhang has discovered a new class of transposon-encoded RNA-guided DNA nucleases, which they said could be used for genome editing in human cells and hold potential for biotechnology. In a paper published on Thursday in Science,…

Continue Reading New Class of Transposon-Encoded RNA-Guided Nucleases May Add to Genome Editing Toolbox

Running htseq-count to “grab” long non coding gene_id names

Running htseq-count to “grab” long non coding gene_id names 0 hi all, new to bioinformatics. so bare with me.. I am trying find long non coding RNA from RNA-seq data. As i checked the human gtf file there are 2 different types of long non coding RNA, “lnc_RNA” and “lncRNA”,…

Continue Reading Running htseq-count to “grab” long non coding gene_id names

where do I find transcript_biotype

where do I find transcript_biotype 1 Hi newbie_r, I am unsure; however, via biomaRt in R, one can generate a master table that has biotypes for Ensembl and RefSeq ‘transcripts’. require(biomaRt) ensembl <- useMart(‘ensembl’, dataset=”hsapiens_gene_ensembl”) annot <- getBM( attributes = c( ‘hgnc_symbol’, ‘ensembl_gene_id’, ‘ensembl_transcript_id’, ‘entrezgene_id’, ‘refseq_mrna’, ‘gene_biotype’), mart = ensembl)…

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ASM287662v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/10/2016 16:40:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,675 CDS (total)::3,608 Genes (coding)::3,557 CDS (coding)::3,557 Genes (RNA)::67 rRNAs::2, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…

Continue Reading Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer