Frequency Analysis of the Splice Site Regions in Different Organisms

Summary We have carried out a comparative analysis of the sub-sequences of size six| ten at the (donor| acceptor) splice site regions of five different organisms. The frequency analysis of the unique sub-sequences at the donor and acceptor regions suggests that the distribution of their occurrence is approximately exponential. We have observed that the number of unique sub-sequences (occurring with different frequencies) at the donor region are less than at the acceptor, suggesting that the sub-sequences at the acceptor region are more variable. The sub-sequences with high percentage of occurrence (uniqueness) are considered to be highly involved in splicing. Our analysis suggests that sub-sequences of length ~6-8 nucleotides (nt) at the splice sites – with six bases in intron (including the two central, conserved dinucleotides) and two bases in exon are optimal for the efficient assembly and binding of the spliceosomal complex during the process of splicing. The score pattern obtained by the alignment of the nucleotides at the donor region with the acceptor and vice-versa also suggests that a single sub-sequence at the donor region have different degree of similarity with sub-sequences at the acceptor thus determining that the donor sub-sequences are more crucial in pairing with the corresponding acceptor sub-sequences during the process of splicing.

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The effect of disease-associated HRPT2 mutations on splicing

Journal of Endocrinology ◽

10.1677/joe-09-0038 ◽

2009 ◽

Vol 201 (3) ◽

pp. 387-396 ◽

Cited By ~ 8

Author(s):

Michael A Hahn ◽

Julie McDonnell ◽

Deborah J Marsh

Keyword(s):

Splice Site ◽

Hot Spot ◽

Splice Sites ◽

Loss Of Function ◽

Splice Enhancer ◽

Aberrant Splicing ◽

Acceptor Splice Site ◽

Web Based ◽

Exonic Splice

Mutations in the tumour suppressor HRPT2 occur in patients with parathyroid carcinoma, kidney tumours and Hyperparathyroidism–Jaw Tumour syndrome. Disruption of exonic splicing through mutation of donor/acceptor splice sites or exonic splice enhancer (ESE) sites leads to loss of function of a number of major tumour suppressors including BRCA1, APC and MLH1. Given that the effect of HRPT2 mutations on splicing has not been widely studied, we used an in vitro splicing assay to determine whether 17 HRPT2 mutations located in hot-spot and other exons predicted to disrupt ESE consensus sites led to aberrant splicing. Using two independent web-based prediction programs, the majority of these mutations were predicted to disrupt ESE consensus sites; however, aberrant splicing of HRPT2 transcripts was not observed. Canonical donor or acceptor splice site mutations were also investigated using this splicing assay and transcripts assessed from tumour tissue. Splice site mutations were shown to lead to either exon skipping or retention of intronic sequences through the use of cryptic splice sites comprised of non-classical splicing signals. Aberrant splicing caused by disruption of ESE sites does not appear to have a major role in HRPT2-associated disease; however, premature truncation of parafibromin as the result of canonical donor or acceptor splice site mutations is associated with pathogenicity. Functional splicing assays must be undertaken in order to confirm web-based software predictions of the modification of putative ESE sites by disease-associated mutations.

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Predicting the effect of variants on splicing using Convolutional Neural Networks

PeerJ ◽

10.7717/peerj.9470 ◽

2020 ◽

Vol 8 ◽

pp. e9470

Author(s):

Thanyathorn Thanapattheerakul ◽

Worrawat Engchuan ◽

Jonathan H. Chan

Keyword(s):

Splice Site ◽

Predictive Models ◽

Rna Splicing ◽

Messenger Rna ◽

Computational Models ◽

Splice Variants ◽

Splice Sites ◽

Splice Site Prediction ◽

Donor And Acceptor ◽

Rna Splice Sites

Mutations that cause an error in the splicing of a messenger RNA (mRNA) can lead to diseases in humans. Various computational models have been developed to recognize the sequence pattern of the splice sites. In recent studies, Convolutional Neural Network (CNN) architectures were shown to outperform other existing models in predicting the splice sites. However, an insufficient effort has been put into extending the CNN model to predict the effect of the genomic variants on the splicing of mRNAs. This study proposes a framework to elaborate on the utility of CNNs to assess the effect of splice variants on the identification of potential disease-causing variants that disrupt the RNA splicing process. Five models, including three CNN-based and two non-CNN machine learning based, were trained and compared using two existing splice site datasets, Genome Wide Human splice sites (GWH) and a dataset provided at the Deep Learning and Artificial Intelligence winter school 2018 (DLAI). The donor sites were also used to test on the HSplice tool to evaluate the predictive models. To improve the effectiveness of predictive models, two datasets were combined. The CNN model with four convolutional layers showed the best splice site prediction performance with an AUPRC of 93.4% and 88.8% for donor and acceptor sites, respectively. The effects of variants on splicing were estimated by applying the best model on variant data from the ClinVar database. Based on the estimation, the framework could effectively differentiate pathogenic variants from the benign variants (p = 5.9 × 10−7). These promising results support that the proposed framework could be applied in future genetic studies to identify disease causing loci involving the splicing mechanism. The datasets and Python scripts used in this study are available on the GitHub repository at https://github.com/smiile8888/rna-splice-sites-recognition.

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HS3D, A DATASET OF HOMO SAPIENS SPLICE REGIONS, AND ITS EXTRACTION PROCEDURE FROM A MAJOR PUBLIC DATABASE

International Journal of Modern Physics C ◽

10.1142/s0129183102003796 ◽

2002 ◽

Vol 13 (08) ◽

pp. 1105-1117 ◽

Cited By ~ 29

Author(s):

PASQUALE POLLASTRO ◽

SALVATORE RAMPONE

Keyword(s):

Splice Site ◽

Prediction Accuracy ◽

Nuclear Dna ◽

Homo Sapiens ◽

Extraction Procedure ◽

Splice Sites ◽

Public Database ◽

Gene Characterization ◽

Donor And Acceptor ◽

The University

The aim of this work is to describe a cleaning procedure of GenBank data, producing material to train and to assess the prediction accuracy of computational approaches for gene characterization. A procedure (GenBank2HS3D) has been defined, producing a dataset (HS3D — Homo Sapiens Splice Sites Dataset) of Homo Sapiens Splice regions extracted from GenBank (Rel.123 at this time). It selects, from the complete GenBank Primate Division, entries of Human Nuclear DNA according with several assessed criteria; then it extracts exons and introns from these entries (actually 4523 + 3802). Donor and acceptor sites are then extracted as windows of 140 nucleotides around each splice site (3799 + 3799). After discarding windows not including canonical GT–AG junctions (65 + 74), including insufficient data (not enough material for a 140 nucleotide window) (686 + 589), including not AGCT bases (29 + 30), and redundant (218 + 226), the remaining windows (2796 + 2880) are reported in the dataset. Finally, windows of false splice sites are selected by searching canonical GT–AG pairs in not splicing positions (271 937 + 332 296). The false sites in a range +/- 60 from a true splice site are marked as proximal. HS3D, release 1.2 at this time, is available at the Web server of the University of Sannio: .

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Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2005.10.009 ◽

2006 ◽

Vol 30 (1) ◽

pp. 50-57 ◽

Cited By ~ 11

Author(s):

Sayed-Amir Marashi ◽

Hani Goodarzi ◽

Mehdi Sadeghi ◽

Changiz Eslahchi ◽

Hamid Pezeshk

Keyword(s):

Neural Networks ◽

Secondary Structure ◽

Splice Site ◽

Rna Secondary Structure ◽

Secondary Structure Information ◽

Acceptor Splice Site ◽

Structure Information ◽

Donor And Acceptor

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The effects of defective Suppressor-mutator insertions on the expression of a Bronze-1 allele in maize

Genome ◽

10.1139/g89-171 ◽

1989 ◽

Vol 31 (2) ◽

pp. 980-986

Author(s):

Hwa Yeong Kim ◽

Victor Raboy ◽

John W. Schiefelbein ◽

Oliver E. Nelson

Keyword(s):

Enzymatic Activity ◽

Transposable Element ◽

Splice Site ◽

Splice Sites ◽

Base Pairs ◽

Acceptor Splice Site ◽

Biochemical Analyses ◽

Bronze Locus ◽

Maize Transposable Element ◽

Mutator Element

Molecular and biochemical analyses of the maize transposable element mutant bronze-m13, which resulted from the insertion of a defective Suppressor-mutator element in an exon of a Bronze-1 allele, and of changes of state derived from bronze-m13 by internal deletions within the element have revealed how these mutant alleles condition a nonmutant phenotype in the absence of a trans-active Suppressor-mutator. The transposable element insertions are all in the same position, 38 base pairs 3′ to the single intron present in the bz locus. The insertions are transcribed with the gene, and the pre-mRNAs of bronze-m13 and CS1, CS5, CS6, and CS12 are then spliced using the intron donor splice site and either one of two acceptor splice sites in the defective Suppressor-mutator element. Only one of these two messages is translated to yield a functional enzyme. The pre-mRNA of CS9 is spliced only in the reaction that gives a translatable message since the pre-mRNA lacks the alternate acceptor splice site. The splicing reactions are detailed and related to the very different amounts of enzymatic activity produced by these alleles. The presence of an antisense message in CS12 plants to the defective Suppressor-mutator sequence transcribed with the bronze locus is also discussed.Key words: maize transposable element, Suppressor-mutator, splicing.

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Screening for Novel LOX and SOD1 Variants in Keratoconus Patients from Brazil

Journal of Ophthalmic and Vision Research ◽

10.18502/jovr.v15i2.6730 ◽

2020 ◽

Author(s):

Diego Nery Benevides Gadelha ◽

Alex Felipe Barbosa Feitosa ◽

Rafaela Gomes da Silva ◽

Luana Talita Antunes ◽

Matheus Cavalcanti Muniz ◽

...

Keyword(s):

Missense Variant ◽

Splice Sites ◽

Fragment Analysis ◽

Donor And Acceptor ◽

Donor Acceptor ◽

Heterozygous Patient ◽

Potential Impact ◽

The Impact ◽

First Time

Purpose: To investigate the presence of the variants of lysyl oxygenase (LOX) and superoxide dismutase 1 (SOD1) genes in Brazilian patients with advanced keratoconus. Methods: Donor genomic DNA extracted from blood samples was screened for 5’UTR, exonic LOX, and SOD1 variants in a subset of 26 patients presenting with advanced keratoconus (KISA > 1000% and I–S > 2.0) by Sanger sequencing. The impact of non-synonymous amino acid changes was evaluated by SIFT, PMUT, and PolyPhen algorithms. The Mutation Taster tool was used to evaluate the potential impact of formation of new donor and acceptor splice sites in the promoter region of affected volunteers carrying sequence variants. A 7-base SOD1 deletion (IVS2 + 50del7bp) previously associated with keratoconus was screened in 140 patients presenting classical keratoconus by gel fragment analysis, and positive samples were sequenced for confirmation. Results: We found an unreported missense variant in LOX exon 6 in one heterozygous patient, leading to substitution of proline with threonine at residue 392 (p. Thr392Pro) of LOX protein sequence. This mutation was predicted to be potentially damaging to LOX protein. Another LOX variant, Arg158Gln, was also detected in another patient but predicted to be non-pathogenic. Two additional new polymorphisms in LOX 5’UTR region (–116C > T and –58C > T) were found in two patients presenting with advanced keratoconus and were predicted to modulate or create donor/acceptor splice sites in LOX transcripts. Additionally, SOD1 deletion was detected in one patient presenting with severe keratoconus, not in control samples. Conclusion: We described three novel LOX polymorphisms identified for the first time in Brazilian patients with advanced keratoconus, as well as a previously described SOD1 deletion strongly associated with keratoconus. A possible role of these variants in modulating transcript levels in the cornea of affected individual requires further investigation.

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Thermochromic aggregation-induced dual phosphorescence via temperature-dependent sp3-linked donor-acceptor electronic coupling

Nature Communications ◽

10.1038/s41467-021-21676-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Tao Wang ◽

Zhubin Hu ◽

Xiancheng Nie ◽

Linkun Huang ◽

Miao Hui ◽

...

Keyword(s):

Excited State ◽

Room Temperature ◽

Electronic Coupling ◽

Temperature Dependent ◽

Molecular Systems ◽

Donor And Acceptor ◽

Theoretical Investigations ◽

Donor Acceptor ◽

And Control ◽

Two Temperature

AbstractAggregation-induced emission (AIE) has proven to be a viable strategy to achieve highly efficient room temperature phosphorescence (RTP) in bulk by restricting molecular motions. Here, we show that by utilizing triphenylamine (TPA) as an electronic donor that connects to an acceptor via an sp3 linker, six TPA-based AIE-active RTP luminophores were obtained. Distinct dual phosphorescence bands emitting from largely localized donor and acceptor triplet emitting states could be recorded at lowered temperatures; at room temperature, only a merged RTP band is present. Theoretical investigations reveal that the two temperature-dependent phosphorescence bands both originate from local/global minima from the lowest triplet excited state (T1). The reported molecular construct serves as an intermediary case between a fully conjugated donor-acceptor system and a donor/acceptor binary mix, which may provide important clues on the design and control of high-freedom molecular systems with complex excited-state dynamics.

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Comparative Analysis of the Human Dystrophin and Utrophin Gene Structures

Genetics ◽

10.1093/genetics/160.2.793 ◽

2002 ◽

Vol 160 (2) ◽

pp. 793-798

Author(s):

Uberto Pozzoli ◽

Manuela Sironi ◽

Rachele Cagliani ◽

Giacomo P Comi ◽

Alessandra Bardoni ◽

...

Keyword(s):

Comparative Analysis ◽

Splice Sites ◽

Gene Structures ◽

Human Dystrophin

Abstract We present analysis of intronic sequences in the human DMD and UTRN genes. In both genes accumulation of repeated elements could account for intron expansion. Out-of-frame rod-domain exons have stronger splice sites and are separated by significantly longer introns as compared to in-frame exons. These features are unique for the two homologs and not shared by other spectrin superfamily genes.

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Supramolecular Systems Containing B–N Frustrated Lewis Pairs of Tris(pentafluorophenyl)borane and Triphenylamine Derivatives

Organic Materials ◽

10.1055/s-0041-1727235 ◽

2021 ◽

Vol 03 (02) ◽

pp. 174-183

Author(s):

P. Chidchob ◽

S. A. H. Jansen ◽

S. C. J. Meskers ◽

E. Weyandt ◽

N. P. van Leest ◽

...

Keyword(s):

Materials Science ◽

Supramolecular Polymers ◽

Frustrated Lewis Pairs ◽

Paramagnetic Resonance ◽

Donor And Acceptor ◽

Donor Acceptor ◽

Noncovalent Polymers ◽

Electron Paramagnetic ◽

Supramolecular Polymerization ◽

Lewis Pairs

The introduction of a chemical additive to supramolecular polymers holds high potential in the development of new structures and functions. In this regard, various donor- and acceptor-based molecules have been applied in the design of these noncovalent polymers. However, the incorporation of boron–nitrogen frustrated Lewis pairs in such architectures is still rare despite their many intriguing properties in catalysis and materials science. The limited choices of suitable boron derivatives represent one of the main limitations for the advancement in this direction. Here, we examine the use of the commercially available tris(pentafluorophenyl)borane with various triphenylamine derivatives to create supramolecular B–N charge transfer systems. Our results highlight the importance of a proper balance between the donor/acceptor strength and the driving force for supramolecular polymerization to achieve stable, long-range ordered B–N systems. Detailed analyses using electron paramagnetic resonance and optical spectroscopy suggest that tris(pentafluorophenyl)borane displays complex behavior with the amide-based triphenylamine supramolecular polymers and may interact in dimers or larger chiral aggregates, depending on the specific structure of the triphenylamines.

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