第一类内含子结构的比较数据库。
A comparative database of group I intron structures.
作者信息
Damberger S H, Gutell R R
机构信息
MCD Biology, University of Colorado, Boulder 80309-0347.
出版信息
Nucleic Acids Res. 1994 Sep;22(17):3508-10. doi: 10.1093/nar/22.17.3508.
Abstract
We have created a database of comparatively derived group I intron secondary structure diagrams. This collection currently contains a broad sampling of phylogenetically and structurally similar and diverse structures from over 200 publicly available intron sequences. As more group I introns are sequenced and added to the database, we anticipate minor refinements in these secondary structure diagrams. These diagrams are directly accessible by computer as well as from the authors.
摘要
我们创建了一个比较推导的I组内含子二级结构示意图数据库。该集合目前包含来自200多个公开可用内含子序列的系统发育和结构上相似及多样结构的广泛样本。随着更多的I组内含子被测序并添加到数据库中，我们预计这些二级结构示意图会有细微的改进。这些示意图可通过计算机直接获取，也可向作者索取。
相似文献
1
A comparative database of group I intron structures.第一类内含子结构的比较数据库。
Nucleic Acids Res. 1994 Sep;22(17):3508-10. doi: 10.1093/nar/22.17.3508.
2
Database on the structure of large ribosomal subunit RNA.大型核糖体亚基RNA结构数据库。
Nucleic Acids Res. 1997 Jan 1;25(1):117-22. doi: 10.1093/nar/25.1.117.
3
Database on the structure of large ribosomal subunit RNA.大核糖体亚基RNA结构数据库。
Nucleic Acids Res. 1994 Sep;22(17):3495-501. doi: 10.1093/nar/22.17.3495.
4
The European Large Subunit Ribosomal RNA Database.欧洲大亚基核糖体RNA数据库。
Nucleic Acids Res. 2001 Jan 1;29(1):175-7. doi: 10.1093/nar/29.1.175.
5
Database on the structure of large ribosomal subunit RNA.大型核糖体亚基RNA结构数据库。
Nucleic Acids Res. 1996 Jan 1;24(1):92-7. doi: 10.1093/nar/24.1.92.
6
Database on the structure of small ribosomal subunit RNA.小核糖体亚基RNA结构数据库。
Nucleic Acids Res. 1994 Sep;22(17):3488-94. doi: 10.1093/nar/22.17.3488.
7
A Group I intron in the nuclear small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: evidence for a new major class of Group I introns.隐皮下腔菌（一种子囊菌）核小亚基rRNA基因中的I组内含子：一类新的主要I组内含子的证据
J Mol Evol. 1999 May;48(5):493-500. doi: 10.1007/pl00006493.
8
The Ribosomal Database Project.核糖体数据库项目
Nucleic Acids Res. 1994 Sep;22(17):3485-7. doi: 10.1093/nar/22.17.3485.
9
Database on the structure of small ribosomal subunit RNA.小核糖体亚基RNA结构数据库。
Nucleic Acids Res. 1996 Jan 1;24(1):86-91. doi: 10.1093/nar/24.1.86.
10
Compilation of small ribosomal subunit RNA structures.小核糖体亚基RNA结构汇编
Nucleic Acids Res. 1993 Jul 1;21(13):3025-49. doi: 10.1093/nar/21.13.3025.
引用本文的文献
1
RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform.RAFFT：使用快速傅里叶变换高效预测 RNA 折叠途径。
PLoS Comput Biol. 2022 Aug 26;18(8):e1010448. doi: 10.1371/journal.pcbi.1010448. eCollection 2022 Aug.
2
Thermodynamic characterization of naturally occurring RNA pentaloops.天然 RNA 五聚体环的热力学特征。
RNA. 2022 Jun;28(6):832-841. doi: 10.1261/rna.078915.121. Epub 2022 Mar 22.
3
Accelerated RNA secondary structure design using preselected sequences for helices and loops.使用预选的螺旋和环序列加速 RNA 二级结构设计。
RNA. 2018 Nov;24(11):1555-1567. doi: 10.1261/rna.066324.118. Epub 2018 Aug 10.
4
Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.基于信息论的 RNA 二级结构 Boltzmann ensemble 的特征描述和可视化。
BMC Bioinformatics. 2018 Mar 5;19(1):82. doi: 10.1186/s12859-018-2078-5.
5
Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.环状结构形成概率的精确计算可识别RNA二级结构中的折叠基序。
RNA. 2016 Dec;22(12):1808-1818. doi: 10.1261/rna.053694.115. Epub 2016 Oct 19.
6
Analysis of secondary structural elements in human microRNA hairpin precursors.人类微小RNA发夹前体中二级结构元件的分析
BMC Bioinformatics. 2016 Mar 1;17:112. doi: 10.1186/s12859-016-0960-6.
7
Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.Dynalign II：用于具有结构域插入的RNA同源物的常见二级结构预测。
Nucleic Acids Res. 2014 Dec 16;42(22):13939-48. doi: 10.1093/nar/gku1172.
8
The intraspecific variability of mitochondrial genes of Agaricus bisporus reveals an extensive group I intron mobility combined with low nucleotide substitution rates.双孢蘑菇线粒体基因的种内变异性揭示了I组内含子的广泛移动性以及低核苷酸替换率。
Curr Genet. 2015 Feb;61(1):87-102. doi: 10.1007/s00294-014-0448-8. Epub 2014 Aug 27.
9
Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops.RNA 2 × 3 核苷酸内环的热力学特征。
Biochemistry. 2012 Jul 3;51(26):5359-68. doi: 10.1021/bi3001227. Epub 2012 Jun 21.
10
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.TurboKnot：快速预测包括伪结在内的保守 RNA 二级结构。
Bioinformatics. 2012 Mar 15;28(6):792-8. doi: 10.1093/bioinformatics/bts044. Epub 2012 Jan 27.
本文引用的文献
1
GenBank.基因银行
Nucleic Acids Res. 1993 Jul 1;21(13):2963-5. doi: 10.1093/nar/21.13.2963.
2
Representation of the secondary and tertiary structure of group I introns.I类内含子二级和三级结构的呈现。
Nat Struct Biol. 1994 May;1(5):273-80. doi: 10.1038/nsb0594-273.
3
Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure.真菌线粒体内含子的比较揭示了RNA二级结构中广泛的同源性。
Biochimie. 1982 Oct;64(10):867-81. doi: 10.1016/s0300-9084(82)80349-0.
4
Making ends meet: a model for RNA splicing in fungal mitochondria.收支平衡：真菌线粒体中RNA剪接的一种模型。
Nature. 1982 Dec 23;300(5894):719-24. doi: 10.1038/300719a0.
5
The intron of the mitochondrial 21S rRNA gene: distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae.线粒体21S rRNA基因的内含子：在不同酵母物种中的分布以及嗜热克鲁维酵母与酿酒酵母之间的序列比较。
Mol Gen Genet. 1983;192(3):487-99. doi: 10.1007/BF00392195.
6
In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence.嗜热四膜虫核糖体RNA前体的体外剪接：鸟苷酸在间隔序列切除中的作用。
Cell. 1981 Dec;27(3 Pt 2):487-96. doi: 10.1016/0092-8674(81)90390-1.
7
Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review.I 组内含子的保守序列和结构：构建 RNA 催化活性位点——综述
Gene. 1988 Dec 20;73(2):259-71. doi: 10.1016/0378-1119(88)90492-1.
8
DNA sequence analysis of the apocytochrome b gene of Podospora anserina: a new family of intronic open reading frame.嗜鸟粪盘菌脱辅基细胞色素b基因的DNA序列分析：一个新的内含子开放阅读框家族
Curr Genet. 1989 Dec;16(5-6):407-18. doi: 10.1007/BF00340720.
9
Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.基于比较序列分析的I组催化内含子三维结构建模。
J Mol Biol. 1990 Dec 5;216(3):585-610. doi: 10.1016/0022-2836(90)90386-Z.
10
Self-splicing of group I introns.I类内含子的自我剪接。
Annu Rev Biochem. 1990;59:543-68. doi: 10.1146/annurev.bi.59.070190.002551.
Zotero 插件