Arabidopsis introns. Medical search. Frequent questions

Although its primary role in basic research has been overshadowed by the more "user-friendly" model species Arabidopsis thaliana , barley retains some peculiar features and has great potential for basic research studies. (mdpi.com)
We analyzed the available data on U12 introns in human and Arabidopsis thaliana genomes in order to systematically compare their conservation with that of U2 introns. (biomedcentral.com)
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)
2003. Genome-wide insertional mutagenesis of Arabidopsis thaliana. (arabidopsis.info)
This file includes the bZIPs protein sequences from Arabidopsis thaliana and six legume genomes (Glycine max,Medicago truncatula,Cajanus cajan,Cicer arietinum,Phaseolus vulgaris and Lotus japonicus). (datadryad.org)
In a genetic screen for suppressors of Arabidopsis (Arabidopsis thaliana) accelerated cell death 6-1 (acd6-1), a small constitutive defense mutant whose defense level is grossly in a reverse proportion to plant size, we identified an allele of the canonical flowering regulatory gene FLOWERING LOCUS K HOMOLOGY DOMAIN (FLK) encoding a putative protein with triple K homology (KH) repeats. (nsf.gov)
Similarly, the first introns of PRF1 and PRF2 in Arabidopsis thaliana were observed to affect constitutive gene expression in vegetative tissues [ 13 ]. (genominfo.org)
The gene encoding 5'-adenylylsulfate (APS) kinase (EC 2.7.1.25) (APK) was cloned from Arabidopsis thaliana. (researchwithrutgers.com)
Lee, S & Leustek, T 1998, ' APS kinase from Arabidopsis thaliana: Genomic organization, expression, and kinetic analysis of the recombinant enzyme ', Biochemical and Biophysical Research Communications , vol. 247, no. 1, pp. 171-175. (researchwithrutgers.com)
Arabidopsis thaliana is known to encode a family of five profilin sequence variants: three vegetative (also constitutive) profilins that are predominantly expressed in all vegetative tissues and ovules, and two reproductive profilins that are specifically expressed in pollen. (biomedcentral.com)
Based on previous phylogenetic analyses in arabidopsis ( Arabidopsis thaliana ), our results showed that some tomato SL-ZH ( S. lycopersicum zinc-finger homeodomain) genes cluster into the same neighbor-joining (NJ) branch as arabidopsis, indicating that these genes may share similar structures and functions in these plants. (ashs.org)
Here, we use a computational approach to perform genome-wide identification and analysis of 611 orthologues of the Arabidopsis thaliana flowering genes. (springer.com)
The B. oleracea being closest to Arabidopsis thaliana is considered an important Brassica species to study polyploidy 8 . (nature.com)

We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. (biomedcentral.com)
The U12 introns, especially, conserved ones are concentrated in 5'-portions of plant and animal genes, where the U12 to U2 conversions occurs preferentially in the 3'-portions of genes. (biomedcentral.com)
Probable orthologs were identified among human and Arabidopsis genes containing U12 introns by BLAST comparison, and the intron positions were mapped onto aligned protein sequences as previously described ([ 16 ] and Additional file 1 ). (biomedcentral.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 legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. (datadryad.org)
1. Identification and characterization of Arabidopsis rat mutants and molecular cloning of RAT genes (Gelvin, Citovsky, Hohn, and Ziemienowicz laboratories, with help from undergraduate students at Tuskegee University). (purdue.edu)
Among the genes affected by FLK is ACD6, whose transcripts had increased intron retentions influenced by the flk mutations. (nsf.gov)
0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. (genominfo.org)
Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. (genominfo.org)
These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters. (genominfo.org)
In addition, we showed that the greater conservation of first introns, associated with a greater number of epigenetic marks, was independent of the conservation of the 5' flanking or promoter regions of genes [ 10 ]. (genominfo.org)
In other words, the signatures that we found in the first introns were not a spillover effect of the promoter or 5′ flanking regions of the genes. (genominfo.org)
Third, we expanded the depth of our analysis to show that genes carrying multiple first-intron TASs constituted a large protein-protein interaction network with each other, ultimately connecting to the UBC protein, which plays a well-established role in ubiquitination. (genominfo.org)
Evidence is presented that combinations of independent function, quantitative genetic effects, and functional redundancy have preserved the three vegetative profilin genes in the Arabidopsis lineage. (biomedcentral.com)
Background: Eukaryotic genes contain non-coding sequences termed introns that intervene between coding sequences. (plantae.org)
Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. (nature.com)

All eukaryotic genomes contain introns within their gene structures [ 1 , 2 ]. (genominfo.org)

SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this splicing factor could be involved in regulation of intron retention. (oregonstate.edu)
The biological functions of intron retention (IR) and nonsense-mediated mRNA decay (NMD) in filamentous fungi is lack of study, let alone their roles in cellulase biosynthesis. (researchsquare.com)
Our results provide better understanding on intron retention, the NMD pathway, and cellulase production mechanism in filamentous fungi. (researchsquare.com)
In intron retention (IR), introns that are supposed to be spliced appear in mature mRNA and subsequently participate in the translation process. (researchsquare.com)
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)
The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, alternative splicing or retention of 4 introns. (blogspot.com)

These results are compatible with the hypothesis that the high level of conservation of U12 intron positions and their persistence in genomes despite the unidirectional U12 to U2 conversion are explained by the role of the slowly excised U12 introns in down-regulation of gene expression. (biomedcentral.com)

Further experiments can specifically point to IME as the cause of expression enhancement - one of the most common is to move the intron upstream of the transcription start site, removing it from the transcript. (wikipedia.org)
Reversely, for every gene the conserved TF binding sites in the upstream/intron/downstream non-coding can also be retrieved. (ugent.be)
In the present work, we sought to provide further evidence on the functionality of first introns, by investigating whether rare alleles located in the sites overlaying epigenomic marks in first introns were more enriched than in 2-kb upstream sequences and other downstream introns. (genominfo.org)

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 U12 introns were mapped onto the genomic sequences yielding 570 human and 182 Arabidopsis U12 validated intron positions available for comparative analysis (Additional file 1 ). (biomedcentral.com)
Alignment of genomic and cDNA sequences revealed that the GPGR5 gene comprises a single open reading frame of 96 amino acids and contains no introns. (tubitak.gov.tr)
Recent high-throughput genomic technologies based on next-generation sequencing have helped to prove that intron sites are in fact subject to natural selection. (genominfo.org)

June 2002 TAIR gene annotation - F10A5.13 Intron. (arabidopsis.info)

Richmond, T. Prediction of intron splice sites. (biomedcentral.com)

Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis. (oregonstate.edu)
Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining (IR) transcripts in Arabidopsis. (oregonstate.edu)
Transcriptomes of nonsense-mediated mRNA decay (NMD)-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. (oregonstate.edu)

Flowering of the reference legume Medicago truncatula is promoted by winter cold (vernalization) followed by long‐day photoperiods (VLD) similar to winter annual Arabidopsis. (nsf.gov)

The interspersed introns can be removed through a large multiprotein splicing complex (the spliceosome) to yield the mature mRNA. (researchsquare.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)
What you see are examples of splicing errors where an intron has not been correctly removed. (blogspot.com)
Arabidopsis mTERF15 is required for mitochondrial nad2 Intron 3 splicing and functional complex I activity. (sinica.edu.tw)
In other words, introns play functional roles in various aspects of molecular dynamics occurring inside cells, such as regulation of gene expression, primary transcript splicing, and mRNA stability [ 9 ]. (genominfo.org)
discover the role of an evolutionarily conserved splicing factor in regulating temperature-responsive flowering in Arabidopsis. (plantae.org)

In Arabidopsis and other plant species, the IMEter has been developed to calculate the likelihood that an intron sequence will enhance gene expression. (wikipedia.org)

Briefly, we investigated whether first introns were conserved to a significantly greater extent than other downstream introns [ 10 ]. (genominfo.org)

Our analysis indicated that on average each Arabidopsis flowering gene has two orthologous copies in quinoa. (springer.com)

A phylogenetic analysis of land plant GSKs indicated that TaSK1 and TaSK2 belong to clade II of plant GSKs, the Arabidopsis members of which are all involved in Brassinosteroid signaling. (biomedcentral.com)
Phylogenetic analysis indicated that CsCAT1-CsCAT3 are closely related to Arabidopsis AtCAT1-AtCAT3, but no obvious counterpart was observed for CsCAT4. (scielo.org)

Intron-mediated enhancement (IME) is the ability of an intron sequence to enhance the expression of a gene containing that intron. (wikipedia.org)
The coding sequence of the gene is composed of 7 exons, interrupted by 6 introns. (researchwithrutgers.com)
Recent completion of the cucumber full-genome sequence has come to facilitate, not only genome-wide analysis of ERF family members in cucumbers themselves, but also a comparative analysis with those in Arabidopsis and rice. (scielo.org)

In multicellular organisms, a pre-mRNA is composed of exons intervened with introns. (researchsquare.com)

To account for plant diversity in terms of functionality, morphology and development, attention has to be devoted to Liliopsida resp Poaceae GSKs in addition to Arabidopsis GSKs. (biomedcentral.com)

Four kinds of intron patterns (a-d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. (datadryad.org)
Intron/exon structure analysis indicated that a few CsERFs still conserved the former intron-position patterns existent in the common ancestor of monocots and eudicots. (scielo.org)

Not all introns enhance gene expression, but those that do can enhance expression between 2- and >1,000-fold relative to an intronless control. (wikipedia.org)
The position of an intron within the transcript is also important - the closer an intron is to the start (5' end) of a transcript, the greater its enhancement of gene expression. (wikipedia.org)
A deletion analysis of this promoter showed that its intron is necessary for the high levels of gene expression. (usda.gov)
In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. (genominfo.org)
We have previously reported some evidence on the functional roles of introns-more specifically, the first ordinally positioned introns (referred to as first introns)-in regulating gene expression [ 10 , 11 ]. (genominfo.org)
Several other recent reports have confirmed the functional importance of introns, particularly first introns, in regulating gene expression. (genominfo.org)
For instance, the first intron of the Col1A1 gene in mice was found to play a role in tissue-specific and developmental gene expression [ 12 ]. (genominfo.org)

Alternative mRNA variants and regulation: The gene contains 29 different introns (28 gt-ag, 1 gc-ag). (blogspot.com)

In particular, the intron must be present in the transcribed region of the gene for enhancement to occur, differentiating IME from the action of typical transcriptional enhancers. (wikipedia.org)

However, the overall level of conservation of U12 introns between plants and animals, and hence the depth of the evolutionary conservation of U12 introns is not known. (biomedcentral.com)

When testing to see whether any given intron enhances the expression of a gene, it is typical to compare the expression of two constructs, one containing the intron and one without it, and to express the difference between the two results as a "fold increase" in enhancement. (wikipedia.org)

The determination of the transcription start site of the UBC gene was found to be dependent on the presence of its first intron [ 14 ]. (genominfo.org)

This study demonstrates the potential application of the GUBQ1 promoter for attaining high levels of transgene expression in Gladiolus and shows the importance of the promoter's intron to expression. (usda.gov)

De K, Bolanos-Villegas P, Mitra S, Yang X, Homan G, Jauh GY, Makaroff CA. The Opposing Actions of Arabidopsis CHROMOSOME TRANSMISSION FIDELITY7 and WINGS APART-LIKE1 and 2 Differ in Mitotic and Meiotic Cells . (sinica.edu.tw)
Bolaños-Villegas P, Yang X, Wang H-J, Ruan C-T, Makaroff CA, Jauh G-Y. Arabidopsis CHROMOSOME TRANSMISSION FIDELITY 7 (AtCTF7/ECO1) is required for meiosis, mitosis and DNA repair. . (sinica.edu.tw)

Descriptions of this phenomenon were first published in cultured maize cells in 1987, and the term "intron-mediated enhancement" was subsequently coined in 1990. (wikipedia.org)

In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. (genominfo.org)

If the intron can no longer enhance expression, then inclusion of the intron in the transcript is important, and the intron probably causes IME. (wikipedia.org)
A significant decrease in GUS expression to background levels occurred in roots and young leaves when the GUBQ1 promoter's entire intron and 5'UTR were deleted. (usda.gov)
Deletion of 70% of the 3'end of the intron resulted in a 50% decrease in expression in callus, roots, and young leaves. (usda.gov)

Besides identification of 99% of the minor introns found in the U12DB, we also discovered ~ 150 new MIGs. (biomedcentral.com)

Intron/exon structure analysis revealed that only one of the 15 positions was completely conserved. (scielo.org)

In that study, we showed that trait-associated single-nucleotide polymorphisms (TASs) were significantly more enriched in first introns than would be expected by random chance. (genominfo.org)

We employed position-weight matrices to obtain a comprehensive updated list of minor introns, consisting of 722 mouse and 770 human minor introns. (biomedcentral.com)
Finally, we identified several novel AS events across minor introns in both mouse and human, which were also tissue-dependent. (biomedcentral.com)

These can be found in the Minor Intron DataBase (MIDB). (biomedcentral.com)
As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. (genominfo.org)

Anatomy36

Organisms31

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20021

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