scholarly journals Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array

2015 ◽  
Vol 62 (5) ◽  
pp. 679-687 ◽  
Author(s):  
Gregory S. Mendez ◽  
Charles F. Delwiche ◽  
Kirk E. Apt ◽  
J. Casey Lippmeier
Keyword(s):  
Gene Structure ◽  
Tandem Array ◽  
Splice Sites ◽  
Intron Splice

scholarly journals Imprecise excision of the Caenorhabditis elegans transposon Tc1 creates functional 5' splice sites.

1994 ◽  
Vol 14 (5) ◽  
pp. 3426-3433 ◽  
Author(s):  
B Carr ◽  
P Anderson
Keyword(s):  
Caenorhabditis Elegans ◽  
Splice Site ◽  
General Characteristic ◽  
Chain Gene ◽  
Splice Sites ◽  
Wild Type ◽  
Reading Frame ◽  
Intron Splice ◽  
Mature Mrna ◽  
Imprecise Excision

Imprecise excision of the Caenorhabditis elegans transposon Tc1 from a specific site of insertion within the unc-54 myosin heavy chain gene generates either wild-type or partial phenotypic revertants. Wild-type revertants and one class of partial revertants contain insertions of four nucleotides in the unc-54 third exon (Tc1 "footprints"). Such revertants express large amounts of functional unc-54 myosin despite having what would appear to be frameshifting insertions in the unc-54 third exon. We demonstrate that these Tc1 footprints act as efficient 5' splice sites for removal of the unc-54 third intron. Splicing of these new 5' splice sites to the normal third intron splice acceptor removes the Tc1 footprint from the mature mRNA and restores the normal translational reading frame. Partial revertant unc-54(r661), which contains a single nucleotide substitution relative to the wild-type gene, is spliced similarly, except that the use of its new 5' splice site creates a frameshift in the mature mRNA rather than removing one. In all of these revertants, two alternative 5' splice sites are available to remove intron 3. We determined the relative efficiency with which each alternative 5' splice site is used by stabilizing frameshifted mRNAs with smg(-) genetic backgrounds. In all cases, the upstream member of the two alternative sites is used preferentially (> 75% utilization). This may reflect an inherent preference of the splicing machinery for the upstream member of two closely spaced 5' splice sites. Creation of new 5' splice sites may be a general characteristic of Tc1 insertion and excision events.

scholarly journals Potential G-quadruplex forming sequences and N6-methyladenosine colocalize at human pre-mRNA intron splice sites

2020 ◽  
Author(s):  
Manuel Jara-Espejo ◽  
Aaron M. Fleming ◽  
Cynthia J. Burrows
Keyword(s):  
Bioinformatic Analysis ◽  
Mrna Splicing ◽  
Published Data ◽  
Splicing Factors ◽  
Splice Sites ◽  
Sequence Context ◽  
Intron Splice ◽  
Alternative Mrna Splicing ◽  
G Quadruplex ◽  
Splice Junctions

ABSTRACTUsing bioinformatic analysis of published data, we identify in human mRNA that potential G-quadruplex forming sequences (PQSs) colocalize with the epitranscriptomic modifications N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). A deeper analysis of the colocalized m6A and PQSs found them intronic in pre-mRNA near 5′ and 3′ splice sites. The loop lengths and sequence context of the m6A-bearing PQSs found short loops most commonly comprised of A nucleotides. This observation is consistent with literature reports of intronic m6A found in SAG (S = C or G) consensus motifs that are also recognized by splicing factors. The localization of m6A and PQSs in pre-mRNA at intron splice junctions suggests that these features could be involved in alternative mRNA splicing. A similar analysis for PQSs around sites of Ψ installation or A-to-I editing in mRNA also found a colocalization; however, the frequency was less than that observed with m6A.TOC Graphic

An algorithm to predict 3′ intron splice sites in Plasmodium falciparum genomic sequences

2001 ◽  
Vol 112 (1) ◽  
pp. 71-77 ◽  
Author(s):  
Robert Huestis ◽  
Nicole Cloonan ◽  
Marina Tchavtchitch ◽  
Allan Saul
Keyword(s):  
Plasmodium Falciparum ◽  
Genomic Sequences ◽  
Splice Sites ◽  
Intron Splice

scholarly journals Floating search methodology for combining classification models for site recognition in DNA sequences

2018 ◽  
Author(s):  
Javier Pérez-Rodríguez ◽  
Aida de Haro-García ◽  
Nicolás García-Pedrajas
Keyword(s):  
Human Genome ◽  
Gene Structure ◽  
Translation Initiation ◽  
Dna Sequences ◽  
Support Vector ◽  
Splice Sites ◽  
Functional Sites ◽  
Stop Codons ◽  
Donor And Acceptor ◽  
Many Sources

AbstractRecognition of the functional sites of genes, such as translation initiation sites, donor and acceptor splice sites and stop codons, is a relevant part of many current problems in bioinformatics. Recognition of the functional sites of genes is also a fundamental step in gene structure predictions in the most powerful programs. The best approaches to this type of recognition use sophisticated classifiers, such as support vector machines. However, with the rapid accumulation of sequence data, methods for combining many sources of evidence are necessary as it is unlikely that a single classifier can solve this type of problem with the best possible performance.A major issue is that the number of possible models to combine is large and the use of all of these models is impractical. In this paper, we present a framework that is based on floating search for combining as many classifiers as needed for the recognition of any functional sites of a gene. The methodology can be used for the recognition of translation initiation sites, donor and acceptor splice sites and stop codons. Furthermore, we can combine any number of classifiers that are trained on any species. The method is also scalable to large datasets, as is shown in experiments in which the whole human genome is used. The method is also applicable to other recognition tasks.We present experiments on the recognition of these four functional sites in the human genome, which is used as the target genome, and use another 20 species as sources of evidence. The proposed methodology shows significant improvement over state-of-the-art methods for use in a thorough evaluation process. The proposed method is also able to improve heuristic selection of species to be used as sources of evidence as the search finds the most useful datasets.Author summaryIn this paper we present a methodology for combining many sources of information to recognize some of the most important functional sites in a genomic sequence. The functional sites of the sequences, such as, translation start sites, translation initiation sites, acceptor and donor splice sites and stop codons, play a very relevant role in many Bioinformatics tasks. Their accurate recognition is an important task by itself and also as part of gene structure prediction programs.Our approach uses a methodology usually termed in Computer Science as “floating search”. This is a powerful heuristics applicable when the cost of evaluating each possible solution is high. The methodology is applied to the recognition of four different functional sites in the human genome using as additional sources of evidence the annotated genomes of other twenty different species.The results show an advantage of the proposed method and also challenge the standard assumption of using only genomes not very close and not very far from the human to improve the recognition of functional sites in the human genome.

scholarly journals Prediction of intron splice sites

2000 ◽  
Vol 1 (1) ◽  
Author(s):  
Todd Richmond
Keyword(s):  
Splice Sites ◽  
Intron Splice

scholarly journals Potential G-Quadruplex Forming Sequences and N6-Methyladenosine Colocalize at Human Pre-mRNA Intron Splice Sites

2020 ◽  
Vol 15 (6) ◽  
pp. 1292-1300 ◽  
Author(s):  
Manuel Jara-Espejo ◽  
Aaron M. Fleming ◽  
Cynthia J. Burrows
Keyword(s):  
Splice Sites ◽  
Intron Splice ◽  
G Quadruplex

Role of small nuclear RNAs in eukaryotic gene expression

2013 ◽  
Vol 54 ◽  
pp. 79-90 ◽  
Author(s):  
Saba Valadkhan ◽  
Lalith S. Gunawardane
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Stability ◽  
Splice Sites ◽  
Branch Site ◽  
Small Nuclear Rnas ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

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