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Journal articles on the topic 'Exons Introns'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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1

Zhu, D. F., Z. H. Hu, and J. M. Shen. "Moult-Inhibiting Hormone from the Swimming Crab, Portunus Trituberculatus (Miers, 1876): PCR Cloning, Tissue Distribution, and Expression of Recombinant Protein in Escherichia Coli (Migula, 1895)." Crustaceana 84, no. 12-13 (2011): 1481–96. http://dx.doi.org/10.1163/156854011x607051.

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AbstractIn the present study, a genomic DNA of MIH (GenBank: #EU869539) was cloned from the swimming crab, Portunus trituberculatus (Miers, 1876). The genome DNA, consisting of 2865 bp, is comprised of three exons interrupted by two introns. Multiple sequence alignments revealed that in the 5 upstream region of MIH, sequences with high similarity to arthropod initiator, TATA box, CREB (cyclic AMP response element binding) protein were the common structure. The signal peptide in the genomic DNA was encoded by exon1 and exon2, which was interrupted by 242 bp-intron (intron1), located between gln

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2

Yan, Liuling, Mrinal Bhave, Robert Fairclough, Christine Konik, Sadequr Rahman, and Rudi Appels. "The genes encoding granule-bound starch synthases at the waxy loci of the A, B, and D progenitors of common wheat." Genome 43, no. 2 (2000): 264–72. http://dx.doi.org/10.1139/g99-117.

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Three genes encoding granule-bound starch synthase (wx-TmA, wx-TsB, and wx-TtD) have been isolated from Triticum monococcum (AA), and Triticum speltoides (BB), by the polymerase chain reaction (PCR) approach, and from Triticum tauschii (DD), by screening a genomic DNA library. Multiple sequence alignment indicated that the wx-TmA, wx-TsB, and wx-TtD genes had the same extron and (or) intron structure as the previously reported waxy gene from barley. The lengths of the three wx-TmA, wx-TsB, and wx-TtD genes were 2834 bp, 2826 bp, and 2893 bp, respectively, each covering 31 bp in the untranslate

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3

Chipens, G., N. Ievina, and I. Kalvinsh. "Internal Regularity of D-Glyceraldehide-3-Phosphate Dehydrogenase Genes and Proteins." Latvian Journal of Chemistry 50, no. 1-2 (2011): 159–64. http://dx.doi.org/10.2478/v10161-011-0061-9.

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Internal Regularity ofD-Glyceraldehide-3-Phosphate Dehydrogenase Genes and ProteinsData of analysis of some GAPDH family gene exon and intron length (nt) and intron position coordinates as a sum of preceeding exon dimensions) and their internal regularity were analyzed based on a working hypothesis that primieval gene precursors were regular and periodic polynucleotides formed from oligonucleotides identical in size. The number of nucleotides in a gene repeat unit was denoted by a specific term - gene quantum and symbolQ. The following genes were analyzed: the chicken GAPDH (12 exons/11 intron

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4

Long, Manyuan, and Michael Deutsch. "Intron—exon structures of eukaryotic model organisms." Nucleic Acids Research 27, no. 15 (1999): 3219–28. http://dx.doi.org/10.1093/nar/27.15.3219.

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Abstract To investigate the distribution of intron—exon structures of eukaryotic genes, we have constructed a general exon database comprising all available introncontaining genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schizosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila . We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable introns that do not contain correct splice sites, the fi

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5

Patthy, László. "Introns and exons." Current Opinion in Structural Biology 4, no. 3 (1994): 383–92. http://dx.doi.org/10.1016/s0959-440x(94)90108-2.

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6

Wang, Dapeng. "IntronDB: a database for eukaryotic intron features." Bioinformatics 35, no. 21 (2019): 4400–4401. http://dx.doi.org/10.1093/bioinformatics/btz242.

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Abstract Summary The rate and extent of unbalanced eukaryotic intron changes exhibit dynamic patterns for different lineages of species or certain functional groups of genes with varied spatio-temporal expression modes affected by selective pressure. To date, only a few key conserved splicing signals or regulatory elements have been identified in introns and little is known about the remaining intronic regions. To trace the evolutionary trajectory of spliceosomal introns from available genomes under a unified framework, we present IntronDB, which catalogs ∼50 000 000 introns from over 1000 gen

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7

Ham, Kristin A., May Thandar Aung-Htut, Sue Fletcher, and Steve D. Wilton. "Nonsequential Splicing Events Alter Antisense-Mediated Exon Skipping Outcome in COL7A1." International Journal of Molecular Sciences 21, no. 20 (2020): 7705. http://dx.doi.org/10.3390/ijms21207705.

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The COL7A1 gene encodes homotrimer fibrils essential for anchoring dermal and epidermal layers, and pathogenic mutations in COL7A1 can cause recessive or dominant dystrophic epidermolysis bullosa. As a monogenic disease gene, COL7A1 constitutes a potential target for antisense oligomer-mediated exon skipping, a therapy applicable to a growing number of other genetic disorders. However, certain characteristics of COL7A1: many exons, low average intron size, and repetitive and guanine-cytosine rich coding sequence, present challenges to the design of specific and effective antisense oligomers. W

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8

Robberson, B. L., G. J. Cote, and S. M. Berget. "Exon definition may facilitate splice site selection in RNAs with multiple exons." Molecular and Cellular Biology 10, no. 1 (1990): 84–94. http://dx.doi.org/10.1128/mcb.10.1.84.

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Interactions at the 3' end of the intron initiate spliceosome assembly and splice site selection in vertebrate pre-mRNAs. Multiple factors, including U1 small nuclear ribonucleoproteins (snRNPs), are involved in initial recognition at the 3' end of the intron. Experiments were designed to test the possibility that U1 snRNP interaction at the 3' end of the intron during early assembly functions to recognize and define the downstream exon and its resident 5' splice site. Splicing precursor RNAs constructed to have elongated second exons lacking 5' splice sites were deficient in spliceosome assem

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Robberson, B. L., G. J. Cote, and S. M. Berget. "Exon definition may facilitate splice site selection in RNAs with multiple exons." Molecular and Cellular Biology 10, no. 1 (1990): 84–94. http://dx.doi.org/10.1128/mcb.10.1.84-94.1990.

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Interactions at the 3' end of the intron initiate spliceosome assembly and splice site selection in vertebrate pre-mRNAs. Multiple factors, including U1 small nuclear ribonucleoproteins (snRNPs), are involved in initial recognition at the 3' end of the intron. Experiments were designed to test the possibility that U1 snRNP interaction at the 3' end of the intron during early assembly functions to recognize and define the downstream exon and its resident 5' splice site. Splicing precursor RNAs constructed to have elongated second exons lacking 5' splice sites were deficient in spliceosome assem

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10

Talerico, M., and S. M. Berget. "Intron definition in splicing of small Drosophila introns." Molecular and Cellular Biology 14, no. 5 (1994): 3434–45. http://dx.doi.org/10.1128/mcb.14.5.3434.

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Approximately half of the introns in Drosophila melanogaster are too small to function in a vertebrate and often lack the pyrimidine tract associated with vertebrate 3' splice sites. Here, we report the splicing and spliceosome assembly properties of two such introns: one with a pyrimidine-poor 3' splice site and one with a pyrimidine-rich 3' splice site. The pyrimidine-poor intron was absolutely dependent on its small size for in vivo and in vitro splicing and assembly. As such, it had properties reminiscent of those of yeast introns. The pyrimidine-rich intron had properties intermediate bet

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11

Talerico, M., and S. M. Berget. "Intron definition in splicing of small Drosophila introns." Molecular and Cellular Biology 14, no. 5 (1994): 3434–45. http://dx.doi.org/10.1128/mcb.14.5.3434-3445.1994.

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Approximately half of the introns in Drosophila melanogaster are too small to function in a vertebrate and often lack the pyrimidine tract associated with vertebrate 3' splice sites. Here, we report the splicing and spliceosome assembly properties of two such introns: one with a pyrimidine-poor 3' splice site and one with a pyrimidine-rich 3' splice site. The pyrimidine-poor intron was absolutely dependent on its small size for in vivo and in vitro splicing and assembly. As such, it had properties reminiscent of those of yeast introns. The pyrimidine-rich intron had properties intermediate bet

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12

Thomas, B. R., V. S. Ford, E. Pichersky, and L. D. Gottlieb. "Molecular characterization of duplicate cytosolic phosphoglucose isomerase genes in Clarkia and comparison to the single gene in Arabidopsis." Genetics 135, no. 3 (1993): 895–905. http://dx.doi.org/10.1093/genetics/135.3.895.

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Abstract The nucleotide sequence of PgiC1-a which encodes a cytosolic isozymes of phosphoglucose isomerase (PGIC; EC 5.3.1.9) in Clarkia lewisii, a wildflower native to California, is described and compared to the previously published sequence of the duplicate PgiC2-a from the same genome. Both genes have the same structure of 23 exons and 22 introns located in identical positions, and they encode proteins of 569 amino acids. Exon and inferred protein sequences of the two genes are 96.4% and 97.2% identical, respectively. Intron sequences are 88.2% identical. The high nucleotide similarity of

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13

Patthy, László. "Intron-dependent evolution: Preferred types of exons and introns." FEBS Letters 214, no. 1 (1987): 1–7. http://dx.doi.org/10.1016/0014-5793(87)80002-9.

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14

Valhmu, W. B., G. D. Palmer, P. A. Rivers, et al. "Structure of the human aggrecan gene: exon-intron organization and association with the protein domains." Biochemical Journal 309, no. 2 (1995): 535–42. http://dx.doi.org/10.1042/bj3090535.

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The complete exon-intron organization of the human aggrecan gene has been defined, and the exon organization has been compared with the individual domains of the protein core. A yeast artificial chromosome containing the aggrecan gene was selected from the Centre d'Etude du Polymorphisme Humaine yeast artificial chromosome library. A cosmid sulibrary was created from this, and direct sequencing of individual cosmids was used to provide the exon-intron organization. The human aggrecan gene was found to be composed of 19 exons ranging in size from 77 to 4224 bp. Exon 1 is non-coding, whereas exo

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15

Park, Geon, Sook Jin Jang, Dae Soo Moon, Young Jin Park, and Ji Young Huh. "Rapid One-Tube Long PCR-Sequencing for ABO Genotyping From Exons 2 to 7." Blood 116, no. 21 (2010): 1116. http://dx.doi.org/10.1182/blood.v116.21.1116.1116.

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Abstract Abstract 1116 Background: ABO is the most clinically important blood group system in transfusion and transplantation medicine. DNA-based methods for determining the ABO genotype have markedly advanced in recent years and have been increasingly introduced in clinical laboratories. Most studies using sequencing methods for ABO genotyping have focused on exons 6 and 7, ignoring the other exon and intron sequences. Although these approaches usually can distinguish among common ABO alleles, erroneous or ambiguous typing results might be obtained in cases of hybrid and subgroup alleles with

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16

Parra, Marilyn, Gene Yeo, and John G. Conboy. "Intron Retention Mechanisms That Regulate SF3B1 and Mitoferrin Gene Expression during Late Erythropoiesis." Blood 128, no. 22 (2016): 1200. http://dx.doi.org/10.1182/blood.v128.22.1200.1200.

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Abstract Intron retention (IR) regulates hundreds of erythroid genes in a differentiation stage-specific manner during terminal erythropoiesis. Regulated genes include highly expressed RNA binding proteins (RBPs) such as SF3B1, as well as iron transporters (e.g., mitoferrins 1 and 2), and cytoskeletal proteins (e.g., alpha spectrin). Selected IR transcripts are relatively abundant; 25-50% of the above-mentioned transcripts can be polyadenylated, retained in the nucleus, and efficiently spliced at all but one or two introns, thus limiting the amount of translatable cytoplasmic mRNA. We are stud

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17

Gee, Sherry L., Robert L. Lersch, Simon Minovitsky, et al. "An Intron Splicing Enhancer Element, UGCAUG, Is Evolutionarily Conserved near Erythroid Protein 4.1R Exon 16 and Other Tissue-Specific Alternative Exons." Blood 104, no. 11 (2004): 1584. http://dx.doi.org/10.1182/blood.v104.11.1584.1584.

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Abstract Alternative pre-mRNA splicing switches provide an important mechanism for regulating gene expression during differentiation. In differentiating erythroblasts, stage-specific activation of protein 4.1R exon 16 splicing promotes the synthesis of protein isoforms with high affinity for spectrin and actin, which is important for mechanical stabilization of the red cell membrane skeleton. Regulation of this alternative splicing switch is mediated by the interaction of multiple trans-acting splicing factor proteins with cis RNA elements in the pre-mRNA. We previously identified an intron sp

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18

Pimentel, Harold, Marilyn Parra, Sherry Gee, Narla Mohandas, Lior Pachter, and John G. Conboy. "The Erythroid Intron Retention Program Encompasses Developmentally Stable and Dynamic Networks and Regulates Diverse Gene Classes." Blood 126, no. 23 (2015): 3331. http://dx.doi.org/10.1182/blood.v126.23.3331.3331.

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Abstract Computational analysis of RNA-seq data from highly purified human erythroblasts has been instrumental in revealing changes in pre-mRNA splicing during terminal erythropoiesis. Here we report updated studies of intron retention (IR), a type of alternative splicing in which specific introns are retained in otherwise efficiently-processed transcripts, allowing post-transcriptional modulation of cellular mRNA levels. Differences in differentiation stage-specificity, degree of retention, nuclear/cytoplasmic localization, and sensitivity to nonsense-mediated decay (NMD) suggest the existenc

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19

Fukasawa, Kayoko M., and Steven S.-L. Li. "Complete Nucleotide Sequence of the Mouse Lactate Dehydrogenase-A Functional Gene: Comparison of the Exon-Intron Organization of Dehydrogenase Genes." Genetics 116, no. 1 (1987): 99–105. http://dx.doi.org/10.1093/genetics/116.1.99.

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ABSTRACT The complete sequence of 12,851 nucleotides of the mouse lactate dehydrogenase-A (LDH-A) gene has been determined. It includes eight exons, seven introns, promoter and regulatory regions. The B1 repetitive elements present in intron III and VI are oriented in opposite orientation, and they share 72% sequence homology. The exon-intron organization of mouse LDH-Agene is compared with the organizations of other dehydrogenase genes, and the molecular evolution of the nicotinamide adenine dinucleotide binding domains is discussed.

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20

Fieldhouse, Dan, and G. Brian Golding. "The rat adenine phosphoribosyltransferase sequence shows evolutionary rate variation among exons in rodents." Genome 36, no. 6 (1993): 1107–10. http://dx.doi.org/10.1139/g93-147.

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The complete genomic sequence of the rat APRT gene is described and compared with published mammalian sequences. The rat APRT gene organization is typical of other rodent APRTs with five exons, one large intron of 993 bp, and three smaller introns averaging 145 bp. Because complete sequences for mouse and Chinese hamster APRT are also known, it is possible to compare the evolutionary rates of change in the exons with those of the introns. The latter provide one possible estimate of underlying rates of change. It is shown that the APRT exons have differential rates of evolution in rodents and h

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21

Olthof, Anouk M., Alisa K. White, Stephen Mieruszynski, et al. "Disruption of exon-bridging interactions between the minor and major spliceosomes results in alternative splicing around minor introns." Nucleic Acids Research 49, no. 6 (2021): 3524–45. http://dx.doi.org/10.1093/nar/gkab118.

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Abstract Vertebrate genomes contain major (&gt;99.5%) and minor (&lt;0.5%) introns that are spliced by the major and minor spliceosomes, respectively. Major intron splicing follows the exon-definition model, whereby major spliceosome components first assemble across exons. However, since most genes with minor introns predominately consist of major introns, formation of exon-definition complexes in these genes would require interaction between the major and minor spliceosomes. Here, we report that minor spliceosome protein U11-59K binds to the major spliceosome U2AF complex, thereby sup

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22

Sievers, Aaron, Frederik Wenz, Michael Hausmann, and Georg Hildenbrand. "Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes." Genes 9, no. 10 (2018): 482. http://dx.doi.org/10.3390/genes9100482.

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In this study, we pairwise-compared multiple genome regions, including genes, exons, coding DNA sequences (CDS), introns, and intergenic regions of 39 Animalia genomes, including Deuterostomia (27 species) and Protostomia (12 species), by applying established k-mer-based (alignment-free) comparison methods. We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by

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RUZZO, Annamaria, Francesca ANDREONI, and Mauro MAGNANI. "Structure of the human hexokinase type I gene and nucleotide sequence of the 5′ flanking region." Biochemical Journal 331, no. 2 (1998): 607–13. http://dx.doi.org/10.1042/bj3310607.

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This study reports the precise intron/exon boundaries and intron/exon composition of the human hexokinase type I gene. A yeast artificial chromosome containing the hexokinase type I gene was isolated from the yeast artificial chromosome library of the Centre d'Étude du Polymorphisme Humaine. A cosmid sublibrary was created and direct sequencing of the individual cosmids was used to provide the exon/intron organization. The human hexokinase type I gene was found to be composed of 18 exons ranging in size from 63 to 305 bp. Intron 1 is at least 15 kb in length, whereas intron 2 spans at least 10

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24

Holland, J. B., S. J. Helland, N. Sharopova, and D. C. Rhyne. "Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat." Genome 44, no. 6 (2001): 1065–76. http://dx.doi.org/10.1139/g01-110.

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Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Av

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Fincher, Justin A., Gary S. Tyson, and Jonathan H. Dennis. "DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function." International Journal of Genomics 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/167578.

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The regulation of metazoan gene expression occurs in part by pre-mRNA splicing into mature RNAs. Signals affecting the efficiency and specificity with which introns are removed have not been completely elucidated. Splicing likely occurs cotranscriptionally, with chromatin structure playing a key regulatory role. We calculated DNA encoded nucleosome occupancy likelihood (NOL) scores at the boundaries between introns and exons across five metazoan species. We found that (i) NOL scores reveal a sequence-based feature at the introns on both sides of the intron-exon boundary; (ii) this feature is n

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26

Simmonds, Rachel E., and David A. Lane. "Structural and Functional Implications of the Intron/Exon Organization of the Human Endothelial Cell Protein C/Activated Protein C Receptor (EPCR) Gene: Comparison With the Structure of CD1/Major Histocompatibility Complex 1 and 2 Domains." Blood 94, no. 2 (1999): 632–41. http://dx.doi.org/10.1182/blood.v94.2.632.

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Abstract The endothelial cell protein C/activated protein C receptor (EPCR) is located primarily on the surface of the large vessels of the vasculature. In vitro studies suggest that it is involved in the protein C anticoagulant pathway. We report the organization and nucleotide sequence of the human EPCR gene. It spans approximately 6 kbp of genomic DNA, with a transcription initiation point 79 bp upstream of the translation initiation (Met) codon in close proximity to a TATA box and other promoter element consensus sequences. The human EPCR gene has been localized to 20q11.2 and consists of

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Simmonds, Rachel E., and David A. Lane. "Structural and Functional Implications of the Intron/Exon Organization of the Human Endothelial Cell Protein C/Activated Protein C Receptor (EPCR) Gene: Comparison With the Structure of CD1/Major Histocompatibility Complex 1 and 2 Domains." Blood 94, no. 2 (1999): 632–41. http://dx.doi.org/10.1182/blood.v94.2.632.414k24_632_641.

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The endothelial cell protein C/activated protein C receptor (EPCR) is located primarily on the surface of the large vessels of the vasculature. In vitro studies suggest that it is involved in the protein C anticoagulant pathway. We report the organization and nucleotide sequence of the human EPCR gene. It spans approximately 6 kbp of genomic DNA, with a transcription initiation point 79 bp upstream of the translation initiation (Met) codon in close proximity to a TATA box and other promoter element consensus sequences. The human EPCR gene has been localized to 20q11.2 and consists of four exon

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28

VOSS, RICHARD F. "LONG-RANGE FRACTAL CORRELATIONS IN DNA INTRONS AND EXONS." Fractals 02, no. 01 (1994): 1–6. http://dx.doi.org/10.1142/s0218348x94000831.

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Spectral density and random walk methods of analyzing symbolic sequences, such as DNA bases, are compared. Systematic errors in DNA walk analysis, wide variability between samples, and small ensembles cast doubt on previous conclusion that long-range correlations in DNA occur in non-coding (intron) sequences. A new study of all GenBank release 73 annotated features demonstrates that both introns and exons have similar long-range fractal correlations with exponents consistent with previous category averages.

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Xu, Jun, Runsheng Chen, Lunjiang Ling, Ruoun Shen, and Jian Sun. "Coincident indices of exons and introns." Computers in Biology and Medicine 23, no. 4 (1993): 333–43. http://dx.doi.org/10.1016/0010-4825(93)90088-i.

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Pozzoli, Uberto, Manuela Sironi, Rachele Cagliani, Giacomo P. Comi, Alessandra Bardoni, and Nereo Bresolin. "Comparative Analysis of the Human Dystrophin and Utrophin Gene Structures." Genetics 160, no. 2 (2002): 793–98. http://dx.doi.org/10.1093/genetics/160.2.793.

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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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MODARESSI, Said, Katja BRECHTEL, Bruno CHRIST, Kurt JUNGERMANN, and chromosomal localization. "Human mitochondrial phosphoenolpyruvate carboxykinase 2 gene." Biochemical Journal 333, no. 2 (1998): 359–66. http://dx.doi.org/10.1042/bj3330359.

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The mitochodrial (mt) phosphoenolpyruvate carboxykinase 2 (PCK2) gene was isolated by screening a human genomic library with a rat cytosolic (cy) PCK1 cDNA probe comprising sequences from exons 2–9 and by PCR amplification of human genomic DNA spanning consecutive exons with known primer pairs from mtPCK2 cDNA containing sequences from two putative neighbouring exons. The mtPCK2 gene spans approx. 10 kb and consists of ten exons and nine introns. All exon–intron junction sequences match the classical GT/AG rule. Northern blot analysis of poly(A)+ and total RNA from various tissues revealed one

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Wang, Xiao, and Haja N. Kadarmideen. "Characterization of Global DNA Methylation in Different Gene Regions Reveals Candidate Biomarkers in Pigs with High and Low Levels of Boar Taint." Veterinary Sciences 7, no. 2 (2020): 77. http://dx.doi.org/10.3390/vetsci7020077.

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DNA methylation of different gene components, including different exons and introns, or different lengths of exons and introns is associated with differences in gene expression. To investigate the methylation of porcine gene components associated with the boar taint (BT) trait, this study used reduced representation bisulfite sequencing (RRBS) data from nine porcine testis samples in three BT groups (low, medium and high BT). The results showed that the methylation levels of the first exons and first introns were lower than those of the other exons and introns. The first exons/introns of CpG i

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Tuohy, Thérèse M. F., and Joanna Groden. "Exons – Introns = Lexons: In‐frame concatenation of exons by PCR." Human Mutation 12, no. 2 (1998): 122–27. http://dx.doi.org/10.1002/(sici)1098-1004(1998)12:2<122::aid-humu7>3.3.co;2-n.

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Tuohy, Thérèse M. F., and Joanna Groden. "Exons – Introns = Lexons: In-frame concatenation of exons by PCR." Human Mutation 12, no. 2 (1998): 122–27. http://dx.doi.org/10.1002/(sici)1098-1004(1998)12:2<122::aid-humu7>3.0.co;2-w.

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Bell, Martyn V., Alison E. Cowper, Marie-Paule Lefranc, John I. Bell, and Gavin R. Screaton. "Influence of Intron Length on Alternative Splicing of CD44." Molecular and Cellular Biology 18, no. 10 (1998): 5930–41. http://dx.doi.org/10.1128/mcb.18.10.5930.

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ABSTRACT Although the splicing of transcripts from most eukaryotic genes occurs in a constitutive fashion, some genes can undergo a process of alternative splicing. This is a genetically economical process which allows a single gene to give rise to several protein isoforms by the inclusion or exclusion of sequences into or from the mature mRNA. CD44 provides a unique example; more than 1,000 possible isoforms can be produced by the inclusion or exclusion of a central tandem array of 10 alternatively spliced exons. Certain alternatively spliced exons have been ascribed specific functions; howev

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Woody, Jenna L., Andrew J. Severin, Yung-Tsi Bolon, et al. "Gene expression patterns are correlated with genomic and genic structure in soybean." Genome 54, no. 1 (2011): 10–18. http://dx.doi.org/10.1139/g10-090.

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Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling technologies, were generated and analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low expression level, an increase in expression breadth correlated with an increase in transcript size because of an increase in the number of exon

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Graham, I. R., M. Hamshere, and I. C. Eperon. "Alternative splicing of a human alpha-tropomyosin muscle-specific exon: identification of determining sequences." Molecular and Cellular Biology 12, no. 9 (1992): 3872–82. http://dx.doi.org/10.1128/mcb.12.9.3872.

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The human alpha-tropomyosin gene hTMnm has two mutually exclusive versions of exon 5 (NM and SK), one of which is expressed specifically in skeletal muscle (exon SK). A minigene construct expresses only the nonmuscle (NM) isoform when transfected into COS-1 cells and both forms when transfected into myoblasts. Twenty-four mutants were produced to determine why the SK exon is not expressed in COS cells. The results showed that exons NM and SK are not in competition for splicing to the flanking exons and that there is no intrinsic barrier to splicing between the exons. Instead, exon SK is skippe

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Graham, I. R., M. Hamshere, and I. C. Eperon. "Alternative splicing of a human alpha-tropomyosin muscle-specific exon: identification of determining sequences." Molecular and Cellular Biology 12, no. 9 (1992): 3872–82. http://dx.doi.org/10.1128/mcb.12.9.3872-3882.1992.

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The human alpha-tropomyosin gene hTMnm has two mutually exclusive versions of exon 5 (NM and SK), one of which is expressed specifically in skeletal muscle (exon SK). A minigene construct expresses only the nonmuscle (NM) isoform when transfected into COS-1 cells and both forms when transfected into myoblasts. Twenty-four mutants were produced to determine why the SK exon is not expressed in COS cells. The results showed that exons NM and SK are not in competition for splicing to the flanking exons and that there is no intrinsic barrier to splicing between the exons. Instead, exon SK is skippe

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Soodeen-Karamath, Sharon, and Ann M. Verrinder Gibbins. "The chicken stathmin gene and its expression in the embryo." Biochemistry and Cell Biology 78, no. 6 (2000): 703–13. http://dx.doi.org/10.1139/o00-082.

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Stathmin, which functions as an intracellular relay in signal transduction pathways, has been suggested as a potential indicator of pluripotent cells in the early mouse embryo. In this study, chicken stathmin cDNA and genomic DNA were analyzed. In mammals stathmin consists of five exons and four introns; exons 3, 4, and 5 in the mammalian stathmin gene are equivalent to one relatively large exon in the chicken stathmin gene. Introns equivalent to introns 3 and 4 in the mammalian stathmin gene are not present in the counterpart gene in chickens and, although intron 2 was shown to be present in

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Pidpala, O. V., and L. L. Lukash. "The analisis of human MGMT gene orthologous in protests." Faktori eksperimental'noi evolucii organizmiv 22 (September 9, 2018): 345–51. http://dx.doi.org/10.7124/feeo.v22.973.

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Aim. The intron sequences of orthologous О6-methylguanin-DNA methyltransferase (MGMT) genes in Protists on the early stages of their formation in eukaryotic organisms have been analysed. Methods. Homologous regions have been defined by the program BLASTN 2.6.1. Nucleotide sequences of the bacterial and mitochondrial group II introns have been taken from Database for Bacterial Group II Introns. Searching and identifying the MGEs have been realized by using CENSOR. Results. It has been shown that the evolution of the gene does not always coincide with the evolution of the organism. This is shown

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Zhang, Yunting, Yuyun Ye, Leiyu Jiang, et al. "Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry." Genes 11, no. 4 (2020): 427. http://dx.doi.org/10.3390/genes11040427.

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The plant sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs) are key regulators in the interconnection of various signaling pathways. However, little is known about the SnRK family in strawberries. In this study, a total of 26 FvSnRKs including one FvSnRK1, nine FvSnRK2s and 16 FvSnRK3s were identified from the strawberry genome database. They were respectively designated as FvSnRK1.1, FvSnRK2.1 to FvSnRK2.9 and FvSnRK3.1 to FvSnRK3.16, according to the conserved domain of each subfamily and multiple sequence alignment with Arabidopsis. FvSnRK family members were unevenly distribut

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Parra, Marilyn, Benjamin W. Booth, Gene W. Yeo, et al. "SF3B1 Gene Expression in Erythroid Cells Is Regulated By Intron Retention Via a Posttranscriptional Mechanism Involving Cryptic Exons Proposed to Function As Splicing Decoys." Blood 130, Suppl_1 (2017): 931. http://dx.doi.org/10.1182/blood.v130.suppl_1.931.931.

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Abstract Proper expression of the MDS-disease gene, SF3B1, ensures appropriate pre-mRNA splicing in erythroid progenitors and during terminal erythropoiesis. We previously showed that the SF3B1 gene is post-transcriptionally regulated in a differentiation stage-specific manner by intron retention (IR), such that ~50% of its transcripts in mature erythroblasts retain intron 4. Based on new mechanistic studies, we propose a model in which mostly unannotated and noncoding exons within intron 4 function as splicing decoys; i.e., they promote retention of intron 4 by interacting with, and blocking

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Maan Hasan Salih, Adnan F Al-Azzawie, and Akeel Hussain Ali Al-Assie. "Intronic SNPs and Genetic Diseases: A Review." International Journal for Research in Applied Sciences and Biotechnology 8, no. 2 (2021): 267–74. http://dx.doi.org/10.31033/ijrasb.8.2.36.

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Introns qualify as Noncoding nucleotide sequences. In splicing, some segments of the RNA transcript (introns) are eliminated, the other segments (exons) are joining together in the formation of the coding RNAs (mRNA, rRNA and tRNA). Also, Non-coding RNA genes are parts of the intronic. On average, there are 7.8 introns and 8.8 exons per human gene. Single nucleotide polymorphisms (SNPs) are existed in the various positions through the human gene, promoters, alternating regions of exons and introns, terminator, in addition to UTRs, untranslated regions (5'- and 3'-).Therefore, many diseases hav

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Dominski, Z., and R. Kole. "Selection of splice sites in pre-mRNAs with short internal exons." Molecular and Cellular Biology 11, no. 12 (1991): 6075–83. http://dx.doi.org/10.1128/mcb.11.12.6075.

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Model pre-mRNAs containing two introns and three exons, derived from the human beta-globin gene, were used to study the effects of internal exon length on splice site selection. Splicing was assayed in vitro in HeLa nuclear extracts and in vivo during transient expression in transfected HeLa cells. For substrates with internal exons 87, 104, and 171 nucleotides in length, in vitro splicing proceeded via a regular splicing pathway, in which all three exons were included in the spliced product. Primary transcripts with internal exons containing 23, 29, and 33 nucleotides were spliced by an alter

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Dominski, Z., and R. Kole. "Selection of splice sites in pre-mRNAs with short internal exons." Molecular and Cellular Biology 11, no. 12 (1991): 6075–83. http://dx.doi.org/10.1128/mcb.11.12.6075-6083.1991.

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Model pre-mRNAs containing two introns and three exons, derived from the human beta-globin gene, were used to study the effects of internal exon length on splice site selection. Splicing was assayed in vitro in HeLa nuclear extracts and in vivo during transient expression in transfected HeLa cells. For substrates with internal exons 87, 104, and 171 nucleotides in length, in vitro splicing proceeded via a regular splicing pathway, in which all three exons were included in the spliced product. Primary transcripts with internal exons containing 23, 29, and 33 nucleotides were spliced by an alter

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Hertel, Klemens J. "Combinatorial Control of Exon Recognition." Journal of Biological Chemistry 283, no. 3 (2007): 1211–15. http://dx.doi.org/10.1074/jbc.r700035200.

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Pre-mRNA splicing is a fundamental process required for the expression of most metazoan genes. It is carried out by the spliceosome, which catalyzes the removal of noncoding intronic sequences to assemble exons into mature mRNAs prior to export and translation. Given the complexity of higher eukaryotic genes and the relatively low level of splice site conservation, the precision of the splicing machinery in recognizing and pairing splice sites is impressive. Introns ranging in size from <100 up to 100,000 bases are removed efficiently. At the same time, a large number of alternative splicin

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Attanasio, Catia, Armelle David, and Marguerite Neerman-Arbez. "Outcome of donor splice site mutations accounting for congenital afibrinogenemia reflects order of intron removal in the fibrinogen alpha gene (FGA)." Blood 101, no. 5 (2003): 1851–56. http://dx.doi.org/10.1182/blood-2002-03-0853.

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Congenital afibrinogenemia (Mendelian Inheritance in Man #202400) is a rare, autosomal recessive disorder characterized by the complete absence of circulating fibrinogen. Our recent studies on the molecular basis of the disease showed that the most common genetic defect is a donor splice mutation in fibrinogen alpha gene (FGA)intron 4, IVS4+1G>T. Two other FGA donor splice mutations, in intron 1 (IVS1+3A>G) and intron 3 (IVS3+1_+4delGTAA), were identified in afibrinogenemia patients. Because it was impossible to directly study the effect of these mutations on mRNA splicing in patient hep

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YAMADA, Yoichi, Naoki ITANO, Masahiro ZAKO, et al. "The gene structure and promoter sequence of mouse hyaluronan synthase 1 (mHAS1)." Biochemical Journal 330, no. 3 (1998): 1223–27. http://dx.doi.org/10.1042/bj3301223.

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The structure and organization of mouse hyaluronan synthase 1 gene, HAS1 were determined by direct sequencing of λ phage clones carrying the entire gene and by application of the long and accurate (LA)-PCR method to amplify regions encompassing the exon-intron boundaries and all of the exons. This gene spans about 11 kb of genomic DNA and consists of 5 exons and 4 introns. A similarity in the exon-intron organization was found between the genes of mouse HAS1 and Xenopus laevis DG42 which was recently identified as Xenopus hyaluronan synthase. The transcription initiation site was determined by

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Raymond, M., and P. Gros. "Mammalian multidrug-resistance gene: correlation of exon organization with structural domains and duplication of an ancestral gene." Proceedings of the National Academy of Sciences 86, no. 17 (1989): 6488–92. http://dx.doi.org/10.1073/pnas.86.17.6488.

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Analysis of the nucleotide and deduced amino acid sequences of the biologically active mouse mdr1 cDNA clone indicates that the protein is formed by two highly homologous halves, each containing six putative transmembrane domains and a nucleotide-binding site. The duplicated unit shows high sequence homology to the proposed energy-coupling subunit of bacterial periplasmic transport proteins. We have cloned and characterized the mouse mdr1 gene and have analyzed the genomic organization of the two homologous halves forming the mdr1 protein. The gene spans 68 kilobases, is split into 28 exons, a

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Chen, Li-hong, Wei Yan, Ting Wang, Yu Wang, Jian Liu, and Zhuo Yu. "Analysis of small and large subunit rDNA introns from several ectomycorrhizal fungi species." PLOS ONE 16, no. 3 (2021): e0245714. http://dx.doi.org/10.1371/journal.pone.0245714.

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The small (18S) and large (28S) nuclear ribosomal DNA (rDNA) introns have been researched and sequenced in a variety of ectomycorrhizal fungal taxa in this study, it is found that both 18S and 28S rDNA would contain introns and display some degree variation in size, nucleotide sequences and insertion positions within the same fungi species (Meliniomyces). Under investigations among the tested isolates, 18S rDNA has four sites for intron insertions, 28S rDNA has two sites for intron insertions. Both 18S and 28S rDNA introns among the tested isolates belong to group I introns with a set of secon

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