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  • 1
    Electronic Resource
    Electronic Resource
    Analysis of Donor Splice Sites in Different Eukaryotic Organisms (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 50 -59 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Donor splice site — Classification — Accuracy — Correlating positions — Functional site
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. We present here a new algorithm for functional site analysis. It is based on four main assumptions: each variation of nucleotide composition makes a different contribution to the overall binding free energy of interaction between a functional site and another molecule; nonfunctioning site-like regions (pseudosites) are absent or rare in genomes; there may be errors in the sample of sites; and nucleotides of different site positions are considered to be mutually dependent. In this algorithm, the site set is divided into subsets, each described by a certain consensus. Donor splice sites of the human protein-coding genes were analyzed. Comparing the results with other methods of donor splice site prediction has demonstrated a more accurate prediction of consensus sequences AG/GU(A,G), G/GUnAG, /GU(A,G)AG, /GU(A,G)nGU, and G/GUA than is achieved by weight matrix and consensus (A,C)AG/GU(A,G)AGU with mismatches. The probability of the first type error, E1, for the obtained consensus set was about 0.05, and the probability of the second type error, E2, was 0.15. The analysis demonstrated that accuracy of the functional site prediction could be improved if one takes into account correlations between the site positions. The accuracy of prediction by using human consensus sequences was tested on sequences from different organisms. Some differences in consensus sequences for the plant Arabidopsis sp., the invertebrate Caenorhabditis sp., and the fungus Aspergillus sp. were revealed. For the yeast Saccharomyces sp. only one conservative consensus, /GUA(U,A,C)G(U,A,C), was revealed (E1 = 0.03, E2 = 0.03). Yeast is a very interesting model to use for analysis of molecular mechanisms of splicing.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006200
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  • 2
    Electronic Resource
    Electronic Resource
    Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin (2005)
    [s.l.] : Nature Publishing Group
    Nature 436 (2005), S. 735-739 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Transcription of eukaryotic genes is performed by three nuclear RNA polymerases, of which RNA polymerase II is thought to be solely responsible for the synthesis of messenger RNAs. Here we show that transcription of some mRNAs in humans and rodents is mediated by a previously unknown ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature03848
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  • 3
    Electronic Resource
    Electronic Resource
    Repetitive DNA Sequences in the Common Vole: Cloning, Characterization and Chromosome Localization of Two Novel Complex Repeats MS3 and MS4 from the Genome of the East European Vole Microtus Rossiaemeridionalis (1998)
    Springer
    Chromosome research 6 (1998), S. 351-360 
    Details
    ISSN: 1573-6849
    Keywords: heterochromatin ; repeats ; sex chromosomes vole
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have characterized two novel, complex, heterochromatic repeat sequences, MS3 and MS4, isolated from Microtus rossiaemeridionalis genomic DNA. Sequence analysis indicates that both repeats consist of unique sequences interrupted by repeat elements of different origin and can be classified as long complex repeat units (LCRUs). A unique feature of both repeat units is the presence of short interspersed repeat elements (SINEs), which are usually characteristic of the euchromatic part of the genome. Comparative analysis revealed no significant stretches of homology in the nucleotide sequences between the two repeats, suggesting that the repeats originated independently during the course of vole genome evolution. Fluorescence in situ hybridization analysis demonstrates that MS3 and MS4 occupy distinct domains in the heterochromatic regions of the sex chromosomes in M. transcaspicus and M. arvalis but collocalize in M. rossiaemeridionalis and M. kirgisorum heterochromatic blocks. The localization pattern of the repeats on the vole chromosomes confirms the independent origin of the two repeats and suggests that expansion of the heterochromatic blocks has occurred subsequent to speciation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009284031287
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  • 4
    Electronic Resource
    Electronic Resource
    B2-like repetitive sequence from the X Chromosome of the American mink (Mustela vison) (1991)
    Springer
    Mammalian genome 1 (1991), S. 165-170 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In analysis of the repeats from the mink X Chromosome (Chr), we have identified a B2-like repetitive sequence of 195 base pairs (bp) flanked by short direct repeats of 14 bp. It contains regions homologous to the split intragenic RNA polymerase III promoter and a 3′ A-rich region followed by an oligo(dA) sequence. A feature of the repeat is the presence of a perfect polypyrimidine tract 22 bp in length absent from the known Alu- and Alu-like sequences. Alignment of the mink B2-like sequence and mouse B2-consensus sequence allowed us to estimate their similarity as 55%. The repeat is present in 1–2×105 copies per mink genome and 2–4×103 copies per X Chr. In situ hybridization analysis demonstrated a similar distribution pattern of the B2-like repeat along the length of all the mink chromosomes including the X. We also observed the presence of mink B2-like hybridizable sequence in the genomes of other Carnivora species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00351063
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  • 5
    Electronic Resource
    Electronic Resource
    LINE-1 element in the vole Microtus subarvalis (1993)
    Springer
    Mammalian genome 4 (1993), S. 624-626 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00361399
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  • 6
    Electronic Resource
    Electronic Resource
    Characterization of several LINE-1 elements in Microtus kirgisorum (1999)
    Springer
    Mammalian genome 10 (1999), S. 724-729 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract. Several LINE-1s have been isolated and characterized from genomic DNA of the vole, Microtus kirgisorum. Blot hybridization revealed specific restriction patterns of L1 elements in vole genomes. Rehybridization of the genomic blot with a cloned 5′-end fragment revealed two major bands indicating the presence of two different L1 subfamilies. The copy numbers are estimated for different parts of M. kirgisorum L1 elements. Data also demonstrate that most vole L1 elements are truncated at the 5′-end; however, in contrast to mouse, the ORF1 copy number is higher in vole. A difference between the substitution rates of the ORF1 5′-region (approximately 330 nucleotides) and the rest of the L1 coding regions is revealed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003359901079
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  • 7
    Electronic Resource
    Electronic Resource
    B2 elements present in the human genome (2000)
    Springer
    Mammalian genome 11 (2000), S. 177-179 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003350010033
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  • 8
    Electronic Resource
    Electronic Resource
    A novel subfamily of LINE-derived elements in mice (1998)
    Springer
    Mammalian genome 9 (1998), S. 881-885 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract. Hybrid sequences have been described previously that consist of a 5′ region homologous to ORF2 of LINEs and a 3′ end that shares homology with a sequence located in the first intron of Cε immunoglobulin. The present investigation has revealed 14 new sequences from seven murine species, that show high homology to those observed earlier. Database search has found several new homologous hybrid sequences including one located in the mouse T-cell receptor (Tcra) locus. Several interesting features of this sequence include identical 15-bp flanking short direct repeats as well as poly-A signal and A-rich sequence at the 3′ end. We have classified this set of sequences as LINE-derived elements (LDEs), which constitute a newly observed subfamily. Comparative analysis of these sequences suggests that a single recombination event was responsible for the production of an LDE progenitor. The phylogenetic tree shows a number of elements that pre-existed in the common ancestor of murine species and displays different evolutionary rates. The time of LDE origin is estimated at approximately 10–15 MYA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003359900887
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular organization and evolution of the D17Leh80-like loci in the mouse t complex (1992)
    Springer
    Mammalian genome 3 (1992), S. 11-16 
    Details
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract We determined the sequence of Tu80, one of the molecular clones derived from microdissected fragments of Chromosome (Chr) 17. The sequence data demonstrated that Tu80 contains an open reading frame (ORF) of 204 bp. Two sequences within the ORF, one homologous to the LINE1 element and the other to the first intron of the C ε gene of mouse immunoglobulin, were observed. A separate sequence, homologous to Tu80, designated as NOV1, was isolated from a genomic library of mouse Chr 17. NOV1 was found to contain an inserted B2 repeat, making it structurally different from Tu80. The sequences of Tu80 and NOV1 were compared with those of LINE1 and the first intron of the C ε gene. The results suggest that the ancestor of the Tu80-like sequence might have arisen through recombination between a LINE1 element and the C ε gene. It is concluded that Tu80 and NOV1 might have resulted from duplication of an ancestral sequence followed by divergence. The comparative analysis also demonstrated a high degree of conservation of the LINE1-like sequence in Tu80 and NOV1. Based on the structure of human, rat, rabbit, and mouse LINE1 fragments, as well as those of NOV1 and Tu80, a phylogenetic tree was constructed. The available data tend to support the assumption that the ancestor for the Tu80-like sequence might have arisen not later than 27–33 million years ago.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00355835
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  • 10
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    Evolutionary switches between two serine codon sets are driven by selection (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-10-31
    Description: Serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. Previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. Here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. The results indicate that the great majority of codon set switches proceed by two consecutive nucleotide substitutions, via a threonine or cysteine intermediate, and are driven by selection. These findings imply a strong pressure of purifying selection in protein evolution, which in the case of serine codon set switches occurs via an initial deleterious substitution quickly followed by a second, compensatory substitution. The result is frequent reversal of amino acid replacements and, at short evolutionary distances, pervasive homoplasy.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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