Intron sequence. Medical search. Frequent questions

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)
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)
Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution. (bcm.edu)
Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis Uniquely among examined arthropods, this predatory mite's Hox genes are completely atomized, dispersed across the genome, and it encodes five copies of the normally single-copy RNA processing Dicer-2 gene. (bcm.edu)
Genes also include regulatory sequences. (livescience.com)
Although scientists don't fully understand their function, regulatory sequences help turn genes on. (livescience.com)
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)
The gene had a structure consisting of 8 introns and 9 exons, similar to other plant AGPGp genes. (usda.gov)
The gene contains 8 introns similar to other ADPGp genes. (usda.gov)
Cladistic analyses based on chloroplast protein coding genes rbcL and rps 4, and the chloroplast encoded trnL (UAA) intron were conducted (1) to investigate phylogenetic relationships among basal peristomate mosses, especially the nematodontous mosses (Tetraphidaceae and Polytrichaceae), and the arthrodontous mosses with pleated endostomes (Buxbaumiaceae and Diphysciaceae), and (2) to make inferences on evolution of the peristome. (bioone.org)
One of the most important aspects of bioinformatics is identifying genes within a long DNA sequence. (genome.gov)
Bioinformatics allows scientists to make educated guesses about where genes are located simply by analyzing sequence data using a computer (in silico). (genome.gov)
Nevertheless, searching for ORFs identifies regions of the DNA sequence that might be parts of genes. (genome.gov)
Most eukaryotic genes take the form of alternating exons and introns. (genome.gov)
Genes are also characterized by specific control sequences that are recognized by enzymes involved with transcription and translation. (genome.gov)
Sequencing of the amplified products was performed to experimentally annotate the NAT-homologous genes and determine their exon-intron structure. (usda.gov)
This document describes some of the target genes and primers that can be used for DNA sequence-based identification of fungi and the PCR conditions with which to use those primers. (cdc.gov)

This sequence does not normally occur in a human or mouse genome. (wikipedia.org)
Rare mutations in genome sequence that result from failed DNA repair are transmitted across generations through DNA replication during each cell division. (nature.com)
Unlike such genetic changes, epigenetic changes, which do not alter genome sequence, can result in three possible outcomes: passive dilution, active repair through negative feedback, or active maintenance through positive feedback. (nature.com)
Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. (nature.com)
A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). (nih.gov)
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)
Whole genome sequence of the Treponema pallidum subsp. (muni.cz)
An attempt is underway to sequence the entire genome of this worm. (grisda.org)
The DNA sequence reported, about 2% of the genome, is one of the largest contiguous DNA sequences known. (grisda.org)
Putative coding sequences account for 29% of the sequenced genome. (grisda.org)
Fourth, inverted repeats are the most common type of repeat, and are located in introns twice as frequently as in other parts of the genome. (grisda.org)
[ 13 ] The mitochondrial genome is remarkably concise, containing little noncoding capacity and no introns. (medscape.com)

With these properties, thermostable group II intron reverse transcriptases are thought to be more advantageous in different biotechnological applications, such as RNA sequencing and qRT-PCR, than widely- adopted retroviral reverse transcriptases. (utexas.edu)
In this dissertation, I begin with evaluating the usage of thermostable group II intron reverse transcriptase end-to-end template-switching activities in rapid preparations of strand-specific, low bias RNA sequencing libraries for the Illumina short-read sequencing platform. (utexas.edu)
By comparing RNA sequencing results from thermostable group II intron reverse transcriptases to that of other widely-adopted commercially-available RNA-seq kits, I demonstrated that this method provided a more accurate and comprehensive measurement of RNA expressions in biological samples. (utexas.edu)
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)

Here we present additional results with the 68 nucleotide fifth intron of the Drosophila myosin heavy chain gene. (umd.edu)
As observed with the 74 nucleotide second intron of the Drosophila white gene, the wild-type myosin intron is accurately spliced in a homologous extract, and increasing the size by 16 nucleotides both eliminates splicing in the Drosophila extract and allows accurate splicing in the human extract. (umd.edu)
In contrast to previous results, however, an upstream cryptic 5' splice site is activated when the wild-type myosin intron is tested in a human HeLa cell nuclear extract, resulting in the removal of a 98 nucleotide intron. (umd.edu)
we noted that a naturally larger (150 nucleotide) intron from the ftz gene is efficiently spliced in Kc cell extracts that do not splice enlarged introns (of 84, 90, 150 or 350 nucleotides) derived from the 74 nucleotide white intron. (umd.edu)
Introns are nucleotide sequences universal amongst the Eukarya domain. (bartleby.com)
1994. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans . (grisda.org)
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. (bvsalud.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)
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)
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)

These primers amplify approximately 495 bp of exons and introns at the 5' end of the β-tubulin gene. (cdc.gov)

While the genomic sequence of DcAOX2a was previously described, we characterize here the complete genomic sequence of DcAOX1 . (frontiersin.org)

This makes it very easy to locate the exact position of the splice site in your sequence. (biomedcentral.com)

The high sequence conservation of HSPC117/RtcB proteins is suggestive of RNA ligase roles of this protein family in various organisms. (nih.gov)
Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. (nih.gov)
Comparison of nuclear-encoded cytoplasmic ribosomal proteins and mitochondrial ribosomal proteins showed that intron positions were conserved (Yoshihama et al. (bartleby.com)

Using RNA sequencing data generated with this novel class of reverse transcriptase, I also showed that current state-of-the-art bioinformatic tools were not optimal for analyzing all RNA classes and biasing against small RNA and RNA with high abundant of mutations and modifications. (utexas.edu)
Finally, I also established an efficient method to prepare high-quality single-stranded DNA sequencing libraries by exploiting the end-to-end template-switching activity and the DNA-dependent, DNA-polymerase activity of this reverse transcriptase and demonstrated its use in liquid biopsies. (utexas.edu)
II intron reverse transcriptase to overcome these obstacles (DM-TGIRT-seq). (cdc.gov)

At least two sequence elements within this region, yet distinct from previously described branchpoint and pyrimidine tract signals, are required for efficient splicing of small hybrid introns in vitro. (umd.edu)

First, intron removal by the tRNA splicing endonuclease generates separate 5' and 3' exons. (nih.gov)
RNA interference-mediated depletion of HSPC117 inhibited maturation of intron-containing pre-tRNA both in vitro and in living cells. (nih.gov)
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)

The NetGene2 server uses a neural network combined with a rule-based system to predict intron splice sites in Arabidopsis thaliana , Caenorhabditis elegans and humans. (biomedcentral.com)

Cells from two severely affected children in family A harbor a homozygous point mutation in XPC intron 3 (-9 T to A), located within the downstream BPS. (yyu.edu.tr)
point mutation at intron 2 leading to splice Description defect Date 10-Feb-1999 (Rel. (lu.se)

Localization of sequences required for size-specific splicing of a small Drosophila intron in vitro. (umd.edu)

The protein that the gene encoded also had many features similar to other plant ADPGp including a variable amino end, conserved catalytic sites and conserved amino acid sequences that control enzyme activity. (usda.gov)
These similarites include introns, histones, several types of RNA polymerase, and methionine as the first amino acid in protein synthesis. (bartleby.com)
The program transcribes each DNA strand into its complementary RNA sequence and then translates the RNA sequence into an amino acid sequence. (genome.gov)
The intron sequences do not code for amino acids and contain internal stop codons. (genome.gov)
This product is synthesized by combining the most common amino acid sequences from all 12 naturally occurring IFNs. (medscape.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)

Sequence of chicken ovalbumin mRNA. (wikidata.org)
The lariat branch point sequence (BPS) is crucial for splicing of human nuclear pre-mRNA yet BPS mutations have infrequently been reported to cause human disease. (yyu.edu.tr)
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. (nih.gov)

Also, the comparison of nucliec acid sequences shows greater similarity between archaea and eukaryotes. (bartleby.com)
Fifth, some sequences with 98% similarity are found widely separated on the chromosome. (grisda.org)

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)
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)

Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. (bvsalud.org)

They suggest that Laparus and especially Neruda may have basal sequences at this locus, which was interesting at the time. (heliconius.org)
However, the power was very low for such low amounts of sequence data, and there was not very strong support for the assertion that Laparus and Neruda are basal to Heliconius . (heliconius.org)
Analysis of the promoter region failed to identify a complete basal promoter but did identify sequences indicating that expression of this gene may respond to various phytohomones and light regimes. (usda.gov)

We performed large-scale sequencing of 600 rice accessions with high diversity, which were collected in 1980 and 2007, using ten unlinked nuclear loci. (springer.com)

These had all been previously screened for the presence of p53 mutations in exons 2 and 4-11 by single strand conformational polymorphism (SSCP) analysis and DNA sequencing as previously described. (bmj.com)

The sequence of this gene is defined by 16 cDNA clones and 18 elements defined by RNA-seq, some from mixed (seen 7 times), embryo (5), l2 (once). (nih.gov)
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)

A cotton gene encoding ADPGp small subunit was isolated and sequenced. (usda.gov)

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

A morphic intron to classify strains by phylogenetic methods. (cdc.gov)

We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. (biomedcentral.com)
We then analyzed the RNAseq data from eleven different mouse tissues, which revealed tissue-specific MIG expression and minor intron retention. (biomedcentral.com)
Moreover, like the major introns, we found that these AS events were more prevalent in long minor introns, while retention was favoured in shorter introns. (biomedcentral.com)
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)
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)

A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. (nih.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)

A total of 16 fungal NAT loci were characterized (4 in F. verticillioides, 3 in F. graminearum, 4 in F. oxysporum, 4 in A. flavus and 1 in A. nidulans), and their sequences were named according to the consensus nomenclature and deposited to the EMBL database. (usda.gov)
There are 7 intronless and 4 segmented NAT loci in Fusaria, while all NAT loci of the Aspergilli contained introns within their coding region. (usda.gov)

This stable silencing requires components of the small RNA pathway and can silence homologous sequences in trans . (nature.com)

In silico sequence analysis of the promoter region of the gene identified motifs associated with light regulation, circadian response, endosperm expression, ethylene response and gibberellic acid response. (usda.gov)

In 2006 I aligned some intronic sequences obtained by Margarita Beltrán and Kanchon Dasmahapatra from Heliconius erato and melpomene group species, together with Laparus and Neruda . (heliconius.org)

Author Manuscript class of cellular RNA for which the standard sequencing methods cannot yet be applied efficiently and quantitatively, although attempts have been made (e.g. ref 2). (cdc.gov)

I have run into problems printing when the data expires from the cache, and I had to resubmit the sequence in order to get a printout. (biomedcentral.com)
Use with SnapGene software or the free Viewer to visualize additional data and align other sequences. (addgene.org)
The GEO accession number for the sequencing data reported in this paper is GSE66550. (cdc.gov)

Here, we have exploited that observation, using a series of hybrid introns to show that a region of 46 nucleotides at the 3' end of the white intron is sufficient to confer the species-specific size effect. (umd.edu)
The sequence lengths vary greatly from approximately 200 basepairs to up to 700 basepairs depending on the species. (cdc.gov)
The Fusarium ID database contains EF1-α sequences for many species of Fusarium . (cdc.gov)

the height of the top of each intron reflects the relative number of clones supporting this intron. (nih.gov)

Likewise, codons for methionine do not always mark the start of a gene sequence. (genome.gov)

Here we report that a minimal combination of cis- regulatory sequences can support permanent RNA silencing of a single-copy transgene and its derivatives in C. elegans simply upon mating. (nature.com)
Recovery is also observed in most cases when double-stranded RNA is used to silence the same coding sequence in different regulatory contexts that drive germline expression. (nature.com)

Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. (nature.com)

There are some potential problems, for example large sequences generate a large number of image files, which may cause memory problems for some browsers. (biomedcentral.com)

Group II intron reverse transcriptases from bacterial thermophiles have high fidelity, processivity and thermostability. (utexas.edu)

Plasmid sequence and annotations. (addgene.org)

any degree of intron conservation in modern eukaryotes is suggestive of function, despite appearing to exist solely for removal. (bartleby.com)

Intron-encoded endonuclease I-Sce I is a homing endonuclease. (wikipedia.org)

2 alleles may have slight differences or the same DNA sequences. (msdmanuals.com)

Anatomy6

Organisms8

Diseases1

Chemicals and Drugs34

Analytical, Diagnostic and Therapeutic Techniques and Equipment15

Phenomena and Processes60

Information Science4

Genes20

Genome13

Thermostable group II intron reve4

Nucleotide7

Genomes5

Exons and introns1

Genomic1

Splice site1

Proteins3

Reverse transcriptase3

Described branchpoint1

TRNA5

Humans1

Point mutation2

Vitro1

Amino6

MRNA3

Similarity2

Familial breast cancer2

Transcription1

Basal3

Accessions1

Polymorphism1

CDNA2

Subunit1

Additionally1

Strains1

Retention5

Boundaries1

Variation1

Loci2

Homologous1

Identified motifs1

Intronic1

Efficiently1

Data3

Species3

Clones1

Methionine1

Regulatory2

Promoter1

Generate1

Group1

Annotations1

Conservation1

Endonuclease1

Alleles1