Intron rna sequence. Medical search. Frequent questions

It is a hepatotropic, approximately 7.2 kb single-stranded positive-sense RNA virus whose genome contains three open reading frames (ORF1, ORF2, and ORF3), 5′ and 3′ untranslated regions (UTRs), and a poly(A) tract at the 3′ end. (nature.com)
Therefore, to capture the heterogeneity of the HEV quasispecies, including recombination events and SNP that occur with very low frequencies, we developed new sequencing approaches for HEV genotype 3 based on the amplification of the near full-length genome of HEV by long-range PCR (lrPCR) followed by subsequent next-generation sequencing (NGS) and third-generation sequencing. (nature.com)
The dynamics of genome replication using deep sequencing. (genomeweb.com)
Therefore, we first wanted to revisit the classification of minor introns in light of the most recent reference genome. (biomedcentral.com)
Hence, the proportion of introns in the LECA genome is considerably greater than in contemporary eukaryotic lineages, excluding some vertebrates (Figure.1). (bartleby.com)
In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1. (researchsquare.com)
The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. (researchsquare.com)
Advances in whole-genome sequencing technologies have enabled numerous key discoveries. (researchsquare.com)
In 1986 Nobel laureate Renato Dulbecco laid down the gauntlet to the scientific community to sequence the complete human genome. (learner.org)
Like the conquest of space, sequencing the human genome required the development of wholly new technologies. (learner.org)
The capstone, of course, was the completion of the human genome sequence. (learner.org)
In 2001 two rival teams jointly announced the completion of a draft sequence of the entire human genome, consisting of more than three billion nucleotides. (learner.org)
One major surprise emerged from the sequencing of the human genome. (learner.org)
Sequencing a genome is an enormous task. (learner.org)
It requires not only finding the nucleotide sequence of small pieces of the genome, but also ordering those small pieces together into the whole genome. (learner.org)
Two general strategies have been used in the sequencing of large genomes: clone-based sequencing and whole genome sequencing (Fig. 1). (learner.org)
One special type of plasmid used for genome sequencing is a bacterial artificial chromosome (BAC) , which can contain DNA fragments of about 150 kb. (learner.org)
Scientists know what they are talking about when they say that the human genome contains about 20,000 protein-coding genes and at least 5,000 genes for non-coding RNAs. (blogspot.com)
Then they confuse themselves by thinking that knowledgeable experts use the word "gene" as a synonym for all functional sequences in the genome. (blogspot.com)
iCLIP of spliceosome components reveals that PRPF8 depletion decreases RNP complex formation at most splice sites in exon-intron junctions throughout the genome. (biomedcentral.com)
In particular, the availability of a sequenced genome, protocols for genome transformation and editing, the presence of a canopy, and a proplastid-to-chloroplast developmental gradient across the leaf blade, together with the unique large collections of natural genetic diversity and mutant populations, make barley a perfect model for chloroplast research. (mdpi.com)
Fast forward to modern-day humans: science has revealed that less than 3% of the human genome is transcribed into messenger RNA (mRNA) molecules that in turn are translated into proteins. (worldhealth.net)
The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. (umd.edu)
The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. (umd.edu)
Using molecular cytogenetics - along with short-read sequencing, optical mapping, linked-read mapping, and long-read genome sequencing - the team found multiple clinically informative breakpoints in two individuals with de novo , karyotypically balanced, rearrangements involving multiple chromosomes and one individual with " de novo , extremely complex" rearrangements centered on chromosome 1. (genomeweb.com)
A Simon Fraser University-led team presents a genome sequence for a virus that pathogenizes a cereal crop pest, the African armyworm ( Spodoptera exempta ), in PLOS One . (genomeweb.com)
In the January issue of the journal Genome Research, two teams of scientists describe a widespread phenomenon in the human genome called transcription-induced chimerism (TIC), where two adjacent genes produce a single, fused RNA transcript. (cshlpress.com)
However, as we deepen our understanding of the eukaryotic genome, a picture emerges that challenges this paradigm - not a picture in which the sequences in the genome have distinct functions, but rather one in which the sequences participate in multiple transcripts, encoding molecules with diverse functionality. (cshlpress.com)
Following a similar whole-genome survey of splicing events, Guig�'s laboratory focused on the ENCODE regions, a set of DNA sequences, representing 1% of the genome, that have been chosen by a large research consortium for more rigorous, in-depth analyses. (cshlpress.com)
Where these repeats occur in the genome matters: during a critical step in gene expression called RNA splicing, only certain pieces (exons) of the RNA transcribed from DNA are joined together to become the final messenger RNA, whereas the remaining RNA sequences (introns) between exons will be broken down. (mcknight.org)
We report here the genome sequence of the Brown Norway (BN) rat strain. (nih.gov)
The sequence represents a high-quality 'draft' covering over 90% of the genome. (nih.gov)
The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. (nih.gov)
This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution. (nih.gov)
[ 13 ] The mitochondrial genome is remarkably concise, containing little noncoding capacity and no introns. (medscape.com)

In vivo, large RNAs rely on proteins to fold to their native conformation. (nih.gov)
Box C/D RNAs are associated with four snoRNP core proteins: NOP56, NOP58, fibrillarin, and 15.5 kDa [ 5 - 7 ]. (hindawi.com)
Box C/D RNAs contain the following functional elements: boxes C and D, which are essential for snoRNA interaction with specific proteins, and a guide sequence that determines the nucleotide to be modified (Figure 1(a) ). (hindawi.com)
Pentatricopeptide repeat (PPR) proteins are sequence-specific RNA-binding proteins that form a pervasive family of proteins conserved in yeast, plants, and humans. (rcsb.org)
For some genes, the abundance of the circular RNA exceeds that of the associated linear mRNA by a factor of 10, raising the interesting possibility that the function of some protein-coding genes may actually be to produce circular noncoding RNAs, not proteins. (bcm.edu)
GeneMark-ETP integrates into GeneMark-ES both types of external information, RNA reads and cross-species proteins. (gatech.edu)
Comparison of nuclear-encoded cytoplasmic ribosomal proteins and mitochondrial ribosomal proteins showed that intron positions were conserved (Yoshihama et al. (bartleby.com)
DNA transcribes into RNA, with exons coding for proteins and introns removed by spliceosomes. (khanacademy.org)
Answering such questions in the cell requires understanding how proteins fit together into a molecular machine such as the spliceosome and how and where they dock onto targets such as RNAs. (mdc-berlin.de)
The method enables a comprehensive evaluation of significantly mutated areas in both coding and noncoding regions of DNA that affect the sites for RNA-binding proteins. (aacr.org)
They seem to think that the gene-centric view requires that everything be attributed to DNA sequences that encode proteins. (blogspot.com)
Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
We identified zebrafish and Fugu TNFSF 13b homologues by genomic DNA database searches and determined that the predicted proteins share 68% and 76% sequence identity with trout TNFSF 13b. (usda.gov)
This process is carried out by the human spliceosome machinery, in which over 300 proteins sequentially assemble with uridine-rich small nuclear RNA molecules (U snRNAs) to form distinct small nuclear ribonucleoprotein complexes (snRNPs). (biomedcentral.com)
In fact, evolutionary biologists hypothesize that RNA existed and self-replicated even before the appearance of DNA and the proteins encoded by it. (worldhealth.net)
However, in some cases, introns with NREs are not broken down, but manage to instruct the making of a variety of repeat proteins that are harmful to nerve cells. (mcknight.org)
In his research, Dr. Guo hopes to uncover how this intron NRE disrupts RNA splicing and causes the production of toxic repeat proteins. (mcknight.org)
Their second aim will test the hypothesis that these changes in the splicing pattern are critical for the C9orf72 NRE RNA to increase its export out from the cell nucleus into the cytoplasm and instruct the making of toxic repeat proteins. (mcknight.org)
The m6A modification modulates alternative splicing patterns by recruiting specific RNA-binding proteins (RBPs) that regulate alternative splicing or by directly influencing the interaction between RBPs and their target RNAs. (bvsalud.org)

Recognition of the intron splice sites is mediated by a base-paired secondary structure of the mRNA that forms at the exon/intron boundaries. (wikipedia.org)
In Saccharomyces cerevisiae the long intron pairs with the 5′ UTR and stalls the ribosomes on the mRNA. (wikipedia.org)
To expand understanding of the role of snoRNAs in control of gene expression, in this study we tested the ability of artificial box C/D RNAs to affect the maturation of target pre-mRNA. (hindawi.com)
The artificial box C/D RNA directed to the branch point adenosine of the second intron, as well as the analogue directed to the last nucleotide of the second exon of the HSPA8 pre-mRNA caused the most prominent influence on the level of HSPA8 mRNAs. (hindawi.com)
Inasmuch as artificial box C/D RNAs decreased viability of transfected human cells, we propose that natural snoRNAs as well as their artificial analogues can influence the maturation of complementary pre-mRNA and can be effective regulators of vital cellular processes. (hindawi.com)
Uppercase letters in the target pre-mRNA sequences correspond to exons, and small letters indicate the intron sequences. (hindawi.com)
MBII-52 box C/D snoRNA containing a guide sequence complementary to the serotonin receptor 2C pre-mRNA was reported to take part in controlling the posttranscriptional modification of the target pre-mRNA (conversion A to I) [ 11 ]. (hindawi.com)
Using such an approach, it was shown that introducing sequences complementary to a selected pre-mRNA into box C/D RNA structures allowed knockdown of the target mRNA [ 13 ]. (hindawi.com)
Genes contain both coding (exon) and non-coding (introns) sections that are transcribed into mRNA. (jax.org)
In total, these results indicate that inhibition or slowing of canonical pre-mRNA processing events shifts the steady-state output of protein-coding genes towards circular RNAs, which likely helps explain why and how circular RNAs show tissue-specific expression profiles. (bcm.edu)
In particular, we are interested in determining how cellular cues can alter the ratio of linear mRNA to circular RNA for a given gene. (bcm.edu)
3 scramble controls were also sequenced as well as mRNA, intron, and lncRNA controls (in singlicate). (nih.gov)
Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. (genomicglossaries.com)
More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
The regulation of expression of X-box-binding protein-1 (XBP1), a transcriptional factor, involves an unconventional mRNA splicing that removes the 26 nucleotides intron. (mdpi.com)
This machinery recognizes pre-mRNA sequences at several motifs - the 5′ and 3′ splice sites, the branch point, and polypyrimidine tracts - positioned at exon-intron boundaries [ 4 ]. (biomedcentral.com)
This includes variants in sequences that regulate messenger RNA (mRNA) splicing and synonymous variants that lead to a change between two codons for the same amino acid, thereby not directly altering the protein-coding sequence. (lu.se)

The bZIP intron RNA motif is an RNA structure guiding splicing of a non-canonical intron from bZIP-containing genes called HAC1 in yeast, XBP1 in Metazoa, Hxl1 or Cib1 in Basidiomycota and bZIP60 in plants. (wikipedia.org)
THA8L resembles THA8 (thylakoid assembly 8), a protein that is required for the splicing of specific group II introns of genes involved in biogenesis of chloroplast thylakoid membranes. (rcsb.org)
Deep sequencing has revealed thousands of eukaryotic protein-coding genes that defy the central dogma, producing circular noncoding RNAs rather than linear messenger RNAs. (bcm.edu)
Upon inhibiting RNA polymerase II termination, circular RNA levels were similarly increased due to readthrough transcripts extending into downstream genes and being subjected to backsplicing. (bcm.edu)
Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). (biomedcentral.com)
Splicing of introns is required for the expression of most eukaryotic genes. (biomedcentral.com)
In these minor intron-containing genes (MIGs), the majority of introns are usually spliced by the major spliceosome, with only one or two introns being spliced by the minor spliceosome. (biomedcentral.com)
Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
have analyzed the tef-1α sequences of F. equiseti , as well as the toxin-related genes PKS13 , PKS4, and TRI5 [26], and Kari has successfully cloned a protease gene [27]. (researchsquare.com)
There are two types of genes: protein-coding genes and those that specify a functional noncoding RNA (i.e ribosomal RNA, lincRNA). (blogspot.com)
Non-experts may not be familiar with the topic and they may have many misconceptions about genes and DNA sequences but we don't base our science on the views of non-experts. (blogspot.com)
METHODS: To identify expressed TNFSF genes, we searched a computer database of ~50,000 rainbow trout expressed sequence tags generated at the National Center for Cool and Cold Water Aquaculture. (usda.gov)
Three introns were identified in the rainbow trout, Atlantic salmon and zebrafish genomic sequences, and the intron locations correspond closely to those in the mammalian TNFSF 13b genes. (usda.gov)
Preferentially retained introns and differentially used exons in the affected genes contain weak 5′ splice sites, but are otherwise indistinguishable from adjacent spliced introns. (biomedcentral.com)
Targeted next-generation sequencing (NGS) of a panel of 80 genes was performed on her initial bone marrow aspirate sample and identified PTPN11, NRAS , and DNMT3A somatic mutations. (frontiersin.org)
Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing. (umd.edu)
In addition, mitochondrial DNA (mtDNA) encodes 2 ribosomal RNA genes and 22 transfer RNA (tRNA) genes necessary for the intramitochondrial synthesis of these 13 polypeptides. (medscape.com)
The proposed mechanism is based on the knowledge that transcription of mtDNA is polycistronic, which means that all genes encoded on the heavy and light strands are transcribed as 2 large precursor RNA strands. (medscape.com)

In the case of the S. cerevisiae group II intron ai5 gamma, the DEAD-box protein Mss116 has been shown to promote the formation of the catalytically active structure. (nih.gov)
Thermostable group II intron reverse transcriptase (TGIRTTM) enzymes and methods for their use are the subject of patents and patent applications that have been licensed by the University of Texas at Austin and East Tennessee State University to InGex, LLC. (cdc.gov)

Splicing of the bZIP intron is a key regulatory step in the unfolded protein response (UPR). (wikipedia.org)
Stem-loop structures around the splice sites and IRE1-specific sequence motifs are both necessary and sufficient for splicing to occur. (wikipedia.org)
G-quadruplexes have been shown to be involved in a range of processes including telomere stability and RNA transcription, splicing, translation and transport. (nature.com)
We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. (biomedcentral.com)
Here we show that minor intron splicing and AS across minor introns is a highly organised process that might be regulated in coordination with the major spliceosome in a tissue-specific manner. (biomedcentral.com)
Regardless, mis-splicing of these few minor introns can have detrimental consequences, as highlighted by diseases caused by mutation in minor spliceosome components. (biomedcentral.com)
The protein binds to RNAs, which suggested that it might participate in splicing. (mdc-berlin.de)
In these cells, the splicing variant will likely directly influence the efficacy of viral RNA clearance in the individual, explaining the impaired clinical outcome in the COVID-19 patient group. (sanger.ac.uk)
In conjunction with RNA sequencing data, the researchers used MIRA to identify mutations in binding sites that altered RNA expression and splicing. (aacr.org)
Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. (biomedcentral.com)
Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5′ splice sites. (biomedcentral.com)
Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5′ splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. (biomedcentral.com)
Scientists are usually more interested in the final, mature RNA sequence after splicing, since that's what results in function (for now ignoring regulatory elements in introns etc. (scienceblogs.com)
RBM10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternative splicing. (crick.ac.uk)
Here, we dissect the RNA code recognized by RBM10 and relate it to the splicing regulatory function of this protein. (crick.ac.uk)
Together, these findings explain RBM10's broad RNA specificity and suggest that RBM10 functions as a splicing regulator using two RNA-binding units with different specificities to promote exon skipping. (crick.ac.uk)
Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends. (yeastgenome.org)
In addition, they discovered that the intergenic sequences of TICs were processed via the same standard eukaryotic splicing machinery that removes introns from RNA transcripts. (cshlpress.com)
Guo and his team will first test a variety of NRE mutations to see which are able to change the splicing pattern so the intron can escape degradation. (mcknight.org)
Our aims are to understand how variants in regulatory motifs control alternative splicing and intron retention and to use this information to develop accurate methods for identification of functional variants. (lu.se)
We are analysing alternative splicing and its association with germline variants and somatic mutations RNA and DNA sequencing data for thousands of women with sporadic or familial breast cancer. (lu.se)
Our main aims are to 1) provide a detailed understanding of how variants in regulatory motifs control alternative splicing and intron retention, and 2) develop accurate methods for identification of functional synonymous variants. (lu.se)

Small nucleolar RNAs (snoRNA) are commonly known to be involved in the processing of precursor ribosomal RNA (pre-rRNA) and small nuclear RNAs (snRNAs). (hindawi.com)
The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). (asm.org)
All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. (umd.edu)

Novel CIC point mutations and an exon-spanning, homozygous deletion identified in oligodendroglial tumors by a comprehensive genomic approach including transcriptome sequencing. (genomeweb.com)
Pathogenic variants can disrupt the splice sites at either end of the exon, create novel splice sites, reveal cryptic splice sites, or disrupt regulatory regions deep within the introns. (jax.org)
However, every exon does not circularize, and, in some cases, multiple exons are present in a circular RNA. (bcm.edu)
SINE elements, in the flanking introns are critical determinants of whether the intervening exon(s) circularize. (bcm.edu)
We propose that this is because cross-exon interactions are not easily replaced with cross-intron interactions, thereby causing spliceosomes to preferentially assemble across an exon and generate a circular RNA. (bcm.edu)
This is a genetic alteration in the DNA sequence at the boundary of an exon and intron. (sanger.ac.uk)
The pinfish tools take minimap2 -spliced alignments and summarise the long-read information into isoforms by clustering reads with similar exon-intron structure. (nanoporetech.com)
We show that a two-domain RRM1-ZnF unit recognizes a GGA-centered motif enriched in RBM10 exonic sites with high affinity and specificity and test that the interaction with these exonic sequences promotes exon skipping. (crick.ac.uk)
Importantly, a second RRM domain (RRM2) of RBM10 recognizes a C-rich sequence, which explains its known interaction with the intronic 3΄ site of NUMB exon 9 contributing to regulation of the Notch pathway in cancer. (crick.ac.uk)

To gain in-depth insights into the viral population and to perform detailed characterization of viral genomes, we used a new approach combining long-range PCR with next-generation and third-generation sequencing which allowed near full-length sequencing of HEV-3 genomes. (nature.com)
Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. (nature.com)
During the past decade, two major developments-the emergence of massively parallel, ultra-cheap DNA sequencing technologies and the use of these technologies as digital readouts for functional genomic assays-have led to a profusion of data describing various features of genomes, epigenomes, and transcriptomes 1 , 2 . (biorxiv.org)
Although they possess many valuable roles this does not explain the ubiquity of introns within eukaryotic genomes. (bartleby.com)
Prior to the development of DNA technology and the sequencing of organismal genomes, Charles Darwin suggested that the "tree" of life can be traced back to a single root (Koonin and Wolf, 2012). (bartleby.com)
This analysis revealed previously unidentified alterations in untranslated regions, long noncoding RNAs, and introns that may guide the interpretation of noncoding variants in cancer genomes. (aacr.org)
By 2003 biologists had sequenced genomes from about one hundred different species. (learner.org)
Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. (umd.edu)
Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). (umd.edu)

Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. (genomeweb.com)

Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. (genomeweb.com)
However, a number of snoRNA-like transcripts do not have guide sequences that are complementary to rRNA or snRNA, so they have unknown functions and are called "orphan snoRNAs" [ 8 , 9 ]. (hindawi.com)

Mutations in these two positively charged patches greatly reduced THA8L RNA-binding activity. (rcsb.org)
Many computational methods for gaining functional insights from sequence data are based on the simple, but powerful, observation that functionally important nucleotides tend to remain unchanged over evolutionary time, because mutations at these sites generally reduce fitness and are therefore eliminated by natural selection 7 - 15 . (biorxiv.org)
To improve our understanding of the biological and clinical significance of somatic mutations on RNA processing in cancer, the authors developed a new method, known as MIRA (mutation identification for RNA alterations). (aacr.org)
Whole-exome sequencing (WES) verified RAD51C, BRIP1, PALB2 , and FANCG heterozygous germline mutations of the FA pathway, which were further confirmed in buccal swab samples by Sanger sequencing. (frontiersin.org)

RNA testing looks for changes in gene expression, and protein analysis assesses structural changes in the protein product of the gene. (jax.org)
Long non-coding RNAs (lncRNAs) are emerging as functional regulators of gene expression in many species1,2. (nih.gov)
Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
Over the last two decades, several laboratories have used a wide range of techniques encompassing expressed sequence tag (EST) analysis, serial analysis of gene expression (SAGE), microarray and next-generation sequencing (NGS) technologies for analysing the chickpea transcriptomes. (intechopen.com)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)
Modern genomics methods produce vast amounts of genetic data, but we have limited ability to interpret the effects of sequence variation on gene expression, protein function and the individual's phenotype. (lu.se)

Novel prokaryotic genomic sequences can be analyzed by the self-training software tool GeneMarkS-2 (sequences longer than 50 Kb). (gatech.edu)

The secondary structure of the bZIP intron is very well conserved, and consists of two hairpins (H2 and H3) around the splice sites, and an extended hairpin (H1) that brings the splice sites together (see figure). (wikipedia.org)
The sequence of the intron is well conserved only around the splice sites. (wikipedia.org)
When repeat sequences from the flanking introns base pair to one another, the splice sites are brought into close proximity and backsplicing occurs. (bcm.edu)

The introns are clipped out of the immature RNA molecule and are not translated into protein. (evcforum.net)
We live in a world made and run by RNA, the equally important sibling of the genetic molecule DNA. (worldhealth.net)
To understand what an individual RNA molecule does, its 3D structure needs to be deciphered at the level of its constituent atoms and molecular bonds. (worldhealth.net)
A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)

On the basis of these data, we constructed a model of THA8L-RNA binding that is dependent on two forces: one is the interaction between nucleotide bases and specific amino acids in the PPR motifs (codes), and the other is the interaction between the negatively charged RNA backbone and positively charged residues of PPR motifs. (rcsb.org)

The nucleotides to be complementary to target nucleotides are shown as C . RNA7D* and RNA8D* were constructed by changing the CUGA sequence in both box D and D′ to AAAA. (hindawi.com)
This is a set of 92 polyadenylated RNAs, ranging from 250 to 2,000 nucleotides in length, which are present in the mixture at defined concentrations. (nanoporetech.com)

The challenge for ID/creationists in this thread is to explain the divergence of exons and introns as measured by sequence comparisons between species. (evcforum.net)

The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. (genomeweb.com)
More recently, another group of researchers reported that they had developed a process for optimizing low- abundance RNA, by combining aRNA amplification with template- switching. (genomicglossaries.com)
cDNA libraries can also be sequenced without any amplification being performed. (nanoporetech.com)
Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)

87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)

More than 150 labs have requested our circular RNA expression plasmids, highlighting our wide impact on this growing field. (bcm.edu)
To study these sequences, they harvest RNA from cells, and reverse transcribe that information using an enzyme called a "reverse transcriptase" to turn that sequence into cDNA, which is more stable, can then be made double stranded, variously manipulated, cloned into plasmids or amplified by techniques like the polymerase chain reaction. (scienceblogs.com)

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. (genomeweb.com)
Transcriptome analysis has been utilized extensively to identify non-coding RNAs such as miRNAs and long intergenic non-coding (LINC) RNAs. (intechopen.com)
Transcriptome analysis has facilitated the development of molecular markers such as simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs) and potential intron polymorphisms (PIPs) that are being used to expedite the chickpea breeding programmes. (intechopen.com)

We identified several putative THA8L-binding sites, enriched with purine sequences, in the group II introns. (rcsb.org)
In silico identification by nucleotide sequence alignment between genomic and cDNA sequences revealed three putative introns in GBSS I. The longest intron was 121 bp long and was located between nucleotide 595 and 716. (scialert.net)

RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
One involved "gluing" the protein onto RNA molecules using a method called PAR-CLIP, provided by Markus Landthaler, extracting RBM20 from cells, and identifying the RNAs attached to it by sequencing them. (mdc-berlin.de)
In contrast, 82% of it is transcribed into RNA molecules with other functions many of which still remain enigmatic. (worldhealth.net)
However, these techniques cannot be applied to RNA molecules with nearly the same effectiveness because their molecular composition and structural flexibility prevent them from easily forming crystals. (worldhealth.net)
Now, a research collaboration led by Wyss Core Faculty member Peng Yin, Ph.D. at the Wyss Institute for Biologically Inspired Engineering at Harvard University, and Maofu Liao, Ph.D. at Harvard Medical School (HMS), has reported a fundamentally new approach to the structural investigation of RNA molecules. (worldhealth.net)
ROCK, as it is called, uses an RNA nanotechnological technique that allows it to assemble multiple identical RNA molecules into a highly organized structure, which significantly reduces the flexibility of individual RNA molecules and multiplies their molecular weight. (worldhealth.net)
ROCK is breaking the current limits of RNA structural investigations and enables 3D structures of RNA molecules to be unlocked that are difficult or impossible to access with existing methods, and at near-atomic resolution," said Yin, who together with Liao led the study. (worldhealth.net)
They hypothesized that such strategies could also be used to assemble naturally occurring RNA molecules into highly ordered circular complexes in which their freedom to flex and move is highly restricted by specifically linking them together. (worldhealth.net)
We speculated that these higher-order rings could be analyzed with high resolution by cryo-EM, which had been applied to RNA molecules with first success. (worldhealth.net)

G-rich sequences have a propensity for forming highly stable quadruplex structures in both RNA and DNA termed G-quadruplexes. (nature.com)

That might not happen if the sequence of an RNA has been altered by a mutation in its gene. (mdc-berlin.de)
point mutation at intron 2 leading to splice Description defect Date 10-Feb-1999 (Rel. (lu.se)

Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)
We applied two strategies to eliminate or substantially reduce the obstacles of tRNA modification and structure for efficient and quantitative tRNA sequencing ( Fig. 1a ). (cdc.gov)

Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. (genomeweb.com)
However, for a discrete number of patients whose results are uninformative, it may be possible to get a more definitive answer about the consequences of a variant using additional methods like RNA sequencing, protein analysis and predictive or functional studies. (jax.org)
Evolutionary turnover may cause inconsistencies between sequence orthology and functional homology that substantially limit this type of analysis. (biorxiv.org)
A gene is a DNA sequence that is transcribed to produce a functional product. (blogspot.com)
However, the molecular mechanisms underlying this seemingly relaxed sequence specificity are not understood and functional studies have focused on 3΄ intronic sites only. (crick.ac.uk)

rRNAs and snRNAs are the main natural targets of 2′-O-methylation that is mediated by box C/D RNAs. (hindawi.com)

After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (genomicglossaries.com)

For identification of the isolated virus, viral RNA was extracted from the supernatants of passaged (passage 2-4) and infected cells. (cdc.gov)
By revealing the fundamental mechanisms by which circular RNAs are generated, we have developed plasmid and viral-based methods for ectopically expressing circular RNAs. (bcm.edu)
The OAS1 gene encodes a protein involved in clearing viral RNA from the cell. (sanger.ac.uk)

II intron reverse transcriptase to overcome these obstacles (DM-TGIRT-seq). (cdc.gov)

RNA sequencing is beginning to show promise for understanding how a DNA variant may disrupt the normal transcription to RNA, post-transcriptional modifications, or the subsequent protein structure. (jax.org)
Tracy says that the poly-A tail helps to promote termination of transcription by the RNA polymerase. (khanacademy.org)
If a promoter were to be after the operator, then a repressor (which binds to the operator) would have no effect on transcription because it would not block the RNA polymerase. (khanacademy.org)
Transcription is controlled by regulatory sequences such as promoters, operators, and enhancers but these are not part of the gene. (blogspot.com)
PCR-cDNA libraries are created by reverse transcription, strand-switching & second-strand synthesis, followed by PCR & attachment of sequencing adapters (Fig. 1a). (nanoporetech.com)

Guanine (G)-quadruplexes are highly stable nucleic acid secondary structures formed from short tracts of G-rich sequence associating together. (nature.com)

These similarites include introns, histones, several types of RNA polymerase, and methionine as the first amino acid in protein synthesis. (bartleby.com)

Population-based Sanger sequencing has been shown to miss minor variants with a frequency below 20% 20 . (nature.com)

In Direct RNA sequencing, adapters are ligated onto the 3' end of poly-A-tailed RNA strands before sequencing (Fig. 1d). (nanoporetech.com)
These subsequently cleave into separate RNA strands, including transfer RNA strands. (medscape.com)

I use the molecular definition since most of what I write refers to DNA sequences. (blogspot.com)
I suspect they are thinking of a gene as coding sequences but you have to struggle to interpret their view of the molecular definition. (blogspot.com)
Now, most of us understand the basics of molecular biology, but all you need to know to understand the significance of this is that DNA is transcribed into RNA, which is then translated into protein. (scienceblogs.com)
In view of the limited understanding of molecular mechanism of m6A and lactylation in As-IPF, MeRIP-seq, RNA-seq and ChIP-seq were analyzed to verify the target gene regulated by m6A and H3K18 lactylation (H3K18la). (bvsalud.org)

Data management and analysis are critical parts of the process, as these sequencing machines generate vast amounts of data. (learner.org)

Importantly, THA8L has strong binding preference for single-stranded RNA over single-stranded DNA or double-stranded RNA. (rcsb.org)

We study this in both sporadic and familial breast cancer, where our work can lead to improvements in the interpretation of clinical sequencing data. (lu.se)

To determine the number of permissible PCR cycles we calculated the variation in sequence counts which could be explained by transcript length, for a PCR-cDNA library created from 1 ng input. (nanoporetech.com)

Knockdown of 17 of these candidates was performed (vs a scramble control) and total RNA was sequenced 48 hours after knockdown. (nih.gov)
17 lncRNAs were selected for knockdown, and RNA was sequenced 48 hours after knockdown (n=1). (nih.gov)

Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution. (genomeweb.com)
Surprisingly, when spliceosome components were depleted or inhibited pharmacologically, the steady-state levels of circular RNAs increased while expression of their associated linear mRNAs concomitantly decreased. (bcm.edu)
We then analyzed the RNAseq data from eleven different mouse tissues, which revealed tissue-specific MIG expression and minor intron retention. (biomedcentral.com)
Using publicly available blood cell RNA sequence and/or array-based expression data for more than 1,000 individuals, the researchers did an expression quantitative trait locus analysis that focused on potential functions for an MS risk SNP within the microRNA miR-548ac, which itself falls in CD58 gene intron. (genomeweb.com)

The spliceosome has to recognize the boundaries between introns and exons in the target RNA and remove the right sequence. (mdc-berlin.de)

However, yeast species have a long (>100 nt) intron in HAC1. (wikipedia.org)
Computational methods predict a bZIP intron with its characteristic RNA structure in 128 out of 156 species studied. (wikipedia.org)
In Fungi a bZIP intron was initially found only in Ascomycota (in 52 out of 63 species analysed) but experimental studies showed it is also present in Basidiomycota and other Candida species. (wikipedia.org)
GeneMark-EP+ integrates into GeneMark-ES information on cross-species protein sequences. (gatech.edu)
Dulbecco also argued that such a project should be "an international undertaking, because the sequence of the human DNA is the reality of the species, and everything that happens in the world depends upon those sequences. (learner.org)
ORG.one Supporting faster, more localised sequencing of critically endangered species. (nanoporetech.com)
When we compare the gene between vertebrate species and look for conserved sequence we find that there are strong signals of sequence conservation that line up with the exons. (evcforum.net)
The third group down is a comparison of the human sequence to specific species with the black bars representing sequence conservation. (evcforum.net)
How does ID/creationism explain this pattern where introns and exons diverge as we move through these species? (evcforum.net)
In 2002, an ad hoc committee for the reevaluation of species definition in bacteriology ( 24 ) advised that all new bacterial species descriptions include an rRNA sequence from the type strain, and in 2001, Bergey's Trust published a revised higher-order taxonomy attempting to reconcile bacterial taxonomy with rRNA-based phylogeny ( 12 , 13 ). (asm.org)

In study by Ono and coworkers, such an antisense element was placed into HBII-180C box C/D RNA instead of the structural element referred to as the M box [ 13 ]. (hindawi.com)
Structural analysis revealed that THA8L contains two extensive patches of positively charged residues next to the residues that are proposed to comprise the RNA-binding codes. (rcsb.org)
Applied to well-known model RNAs with different sizes and functions as benchmarks, the team showed that their method enables the structural analysis of the contained RNA subunits with a technique known as cryo-electron microscopy (cryo-EM). (worldhealth.net)

Additionally, many minor introns were efficiently spliced compared to their flanking major introns. (biomedcentral.com)

Large expansions of a non-coding GGGGCC-repeat in the first intron of the C9orf72 gene are a common cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). (nature.com)
Large expansions of the non-coding GGGGCC-repeat in the first intron of the C9orf72 gene have been recently demonstrated to cause ALS and FTD 5 , 6 . (nature.com)
A well-known example is an intron NRE within a gene called C9orf72, which is the most common genetic cause of amyotrophic lateral sclerosis (ALS, or Lou Gehrig's disease) and frontotemporal dementia (FTD). (mcknight.org)

RNA which contains an intron sequence that has an enzyme- like catalytic activity. (genomicglossaries.com)

Lee (2020) and Frésard (2019) demonstrated clinical utility in adding RNA sequencing to genomic testing for cohorts of individuals with undiagnosed Mendelian disease, increasing the diagnostic yield by 18% and 7.5%, respectively. (jax.org)

Anatomy13

Organisms25

Chemicals and Drugs110

Analytical, Diagnostic and Therapeutic Techniques and Equipment23

Phenomena and Processes88

Disciplines and Occupations1

Technology, Industry, Agriculture1

Information Science11

Health Care1

Genome35

Proteins19

MRNA20

Genes18

Group II int2

Splicing22

Ribosomal3

Exon9

Genomes9

Mitochondrial1

Transcripts2

Mutations4

Gene expression6

Genomic sequences1

Splice sites3

Molecule5

Motifs1

Nucleotides2

Exons and introns1

Amplification4

Polymerase promoter1

Plasmids2

Transcriptome3

Putative2

Molecules9

Termed G-quadruplexes1

Mutation2

TRNA3

Functional5

SnRNAs1

CDNA synthesis1

Viral3

Reverse transcriptase1

Transcription5

Structures1

Synthesis1

Variants1

Strands2

Molecular4

Generate1

Single-stranded1

Familial breast cancer1

Transcript1

Knockdown2

Expression4

Boundaries1

Species10

Structural3

Additionally1

C9orf723

Catalytic1

Clinical1