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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Base Sequence

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Disease relevance of Base Sequence


Psychiatry related information on Base Sequence


High impact information on Base Sequence

  • Somatic diversification of chicken V gene segments occurs by intrachromosomal gene conversion, a DNA recombination process which involves unidirectional transfer of nucleotide sequence blocks from families of V region pseudogenes into the functional rearranged VH and VL genes [8].
  • Here we directly test this hypothesis by comparing global patterns of DNA sequence variation on the Y chromosome and mitochondrial DNA (mtDNA) in the same panel of 389 individuals from ten populations (four from Africa and two each from Europe, Asia and Oceania) [9].
  • Here we use an inducible Xist expression system in mouse embryonic stem cells that recapitulates long-range chromosomal silencing to elucidate which Xist RNA sequences are necessary for chromosomal association and silencing [10].
  • Epistasis analysis showed that Sgs1p is redundant with DNA mismatch repair (MMR) for suppressing GCRs and for suppressing recombination between divergent DNA sequences [11].
  • In addition, the nucleotide sequences of the glycoprotein H gene from the seven CMV isolates were determined [12].

Chemical compound and disease context of Base Sequence


Biological context of Base Sequence

  • The nucleotide sequence is partially corroborated by the sequence of fragments obtained previously from 32P-mRNA fingerprints and endonuclease IV digests of 32P-cDNA, and is in agreement with the amino acid sequence of the constant region, except for a rearrangement of four amino acids (between amino acid positions 163 and 166) [18].
  • Analysis of the nucleotide sequence of the genetic locus for yeast mitochondrial RNA polymerase (RPO41) reveals a continuous open reading frame with the coding potential for a polypeptide of 1351 amino acids, a size consistent with the electrophoretic mobility of this enzymatic activity [19].
  • Plasmid deletions generated with Bal 31 nuclease show that the DNA sequence CTGCCACCC in the -44 to -36 region of this promoter is necessary for its heat shock activity [20].
  • The mitochondrial genome of maize contains a DNA sequence homologous to the chloroplast gene coding for the large subunit of ribulose-1,5-bisphosphate carboxylase (LS gene) [21].
  • We previously defined a family of DNA sequence variants in the core promoter of the gene ALOX5 (on chromosome 10q11.2) associated with diminished promoter-reporter activity in tissue culture [22].

Anatomical context of Base Sequence


Associations of Base Sequence with chemical compounds

  • The DNA sequence revealed a substitution of a cysteine codon for a tyrosine codon at residue 807 in the cytoplasmic domain of the receptor [28].
  • Nucleotide sequence analysis of cloned DNA and electrophoretic analysis of appropriate small fragments from animal tissue reveal a population of length polymorphs containing from nine to 19 cytosine residues [29].
  • In striking contrast to this result, Hae III acted on formaldehyde-fixed minichromosomes to yield only one of the limit-digest fragments, F, which is located in the immediate vicinity of the origin of replication, spanning nucleotides 5169 and 250 on the DNA sequence map of Reddy et al [30].
  • Advantages of this technique include the ease of cloning tyrosine kinase receptor targets present at low levels and the ability to identify proteins that are related in their capacity to bind activated receptors but contain no significant DNA sequence homology [31].
  • Its 77 nucleotide sequence can be folded into a typical cloverleaf structure with a UCU anticodon corresponding to the rare arginine codon AGA [32].

Gene context of Base Sequence


Analytical, diagnostic and therapeutic context of Base Sequence


  1. New topoisomerase essential for chromosome segregation in E. coli. Kato, J., Nishimura, Y., Imamura, R., Niki, H., Hiraga, S., Suzuki, H. Cell (1990) [Pubmed]
  2. Isolation of transforming DNA: cloning the hamster aprt gene. Lowy, I., Pellicer, A., Jackson, J.F., Sim, G.K., Silverstein, S., Axel, R. Cell (1980) [Pubmed]
  3. Bacillus subtilis RNAase III cleavage sites in phage SP82 early mRNA. Panganiban, A.T., Whiteley, H.R. Cell (1983) [Pubmed]
  4. Spliced leader RNA sequences can substitute for the essential 5' end of U1 RNA during splicing in a mammalian in vitro system. Bruzik, J.P., Steitz, J.A. Cell (1990) [Pubmed]
  5. Specific regulation of mRNA splicing in vitro by a peptide from HIV-1 Rev. Kjems, J., Frankel, A.D., Sharp, P.A. Cell (1991) [Pubmed]
  6. Alzheimer's disease associated with mutations in presenilin 2 is rare and variably penetrant. Sherrington, R., Froelich, S., Sorbi, S., Campion, D., Chi, H., Rogaeva, E.A., Levesque, G., Rogaev, E.I., Lin, C., Liang, Y., Ikeda, M., Mar, L., Brice, A., Agid, Y., Percy, M.E., Clerget-Darpoux, F., Piacentini, S., Marcon, G., Nacmias, B., Amaducci, L., Frebourg, T., Lannfelt, L., Rommens, J.M., St George-Hyslop, P.H. Hum. Mol. Genet. (1996) [Pubmed]
  7. V region gene usage and somatic mutation in the primary and secondary responses to influenza virus hemagglutinin. Clarke, S.H., Staudt, L.M., Kavaler, J., Schwartz, D., Gerhard, W.U., Weigert, M.G. J. Immunol. (1990) [Pubmed]
  8. Avian B-cell development: generation of an immunoglobulin repertoire by gene conversion. McCormack, W.T., Tjoelker, L.W., Thompson, C.B. Annu. Rev. Immunol. (1991) [Pubmed]
  9. Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males. Wilder, J.A., Kingan, S.B., Mobasher, Z., Pilkington, M.M., Hammer, M.F. Nat. Genet. (2004) [Pubmed]
  10. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Wutz, A., Rasmussen, T.P., Jaenisch, R. Nat. Genet. (2002) [Pubmed]
  11. SGS1, the Saccharomyces cerevisiae homologue of BLM and WRN, suppresses genome instability and homeologous recombination. Myung, K., Datta, A., Chen, C., Kolodner, R.D. Nat. Genet. (2001) [Pubmed]
  12. Intrauterine transmission of cytomegalovirus to infants of women with preconceptional immunity. Boppana, S.B., Rivera, L.B., Fowler, K.B., Mach, M., Britt, W.J. N. Engl. J. Med. (2001) [Pubmed]
  13. Nucleotide sequence heterogeneity of an RNA phage population. Domingo, E., Sabo, D., Taniguchi, T., Weissmann, C. Cell (1978) [Pubmed]
  14. The regulatory region of the trp operon of Serratia marcescens. Miozzari, G.F., Yanofsky, C. Nature (1978) [Pubmed]
  15. Sequence specificity of trinucleoside diphosphate binding to polymerized tobacco mosaic virus protein. Steckert, J.J., Schuster, T.M. Nature (1982) [Pubmed]
  16. Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Weeks, K.M., Ampe, C., Schultz, S.C., Steitz, T.A., Crothers, D.M. Science (1990) [Pubmed]
  17. Detection of HIV-1 DNA and messenger RNA in individual cells by PCR-driven in situ hybridization and flow cytometry. Patterson, B.K., Till, M., Otto, P., Goolsby, C., Furtado, M.R., McBride, L.J., Wolinsky, S.M. Science (1993) [Pubmed]
  18. Complete sequence of constant and 3' noncoding regions of an immunoglobulin mRNA using the dideoxynucleotide method of RNA sequencing. Hamlyn, P.H., Browniee, G.G., Cheng, C.C., Gait, M.J., Milstein, C. Cell (1978) [Pubmed]
  19. Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Masters, B.S., Stohl, L.L., Clayton, D.A. Cell (1987) [Pubmed]
  20. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Taylor, W.E., Straus, D.B., Grossman, A.D., Burton, Z.F., Gross, C.A., Burgess, R.R. Cell (1984) [Pubmed]
  21. Maize mitochondrial DNA contains a sequence homologous to the ribulose-1,5-bisphosphate carboxylase large subunit gene of chloroplast DNA. Lonsdale, D.M., Hodge, T.P., Howe, C.J., Stern, D.B. Cell (1983) [Pubmed]
  22. Pharmacogenetic association between ALOX5 promoter genotype and the response to anti-asthma treatment. Drazen, J.M., Yandava, C.N., Dubé, L., Szczerback, N., Hippensteel, R., Pillari, A., Israel, E., Schork, N., Silverman, E.S., Katz, D.A., Drajesk, J. Nat. Genet. (1999) [Pubmed]
  23. Repetitive sequences in class-switch recombination regions of immunoglobulin heavy chain genes. Kataoka, T., Miyata, T., Honjo, T. Cell (1981) [Pubmed]
  24. A complex of interacting DNAase I-hypersensitive sites near the Drosophila glue protein gene, Sgs4. Shermoen, A.W., Beckendorf, S.K. Cell (1982) [Pubmed]
  25. Identical V beta T-cell receptor genes used in alloreactive cytotoxic and antigen plus I-A specific helper T cells. Rupp, F., Acha-Orbea, H., Hengartner, H., Zinkernagel, R., Joho, R. Nature (1985) [Pubmed]
  26. MAP2 kinase and 70K S6 kinase lie on distinct signalling pathways. Ballou, L.M., Luther, H., Thomas, G. Nature (1991) [Pubmed]
  27. Expression of a human gene for interferon in yeast. Hitzeman, R.A., Hagie, F.E., Levine, H.L., Goeddel, D.V., Ammerer, G., Hall, B.D. Nature (1981) [Pubmed]
  28. The J.D. mutation in familial hypercholesterolemia: amino acid substitution in cytoplasmic domain impedes internalization of LDL receptors. Davis, C.G., Lehrman, M.A., Russell, D.W., Anderson, R.G., Brown, M.S., Goldstein, J.L. Cell (1986) [Pubmed]
  29. Heterogeneous mitochondrial DNA D-loop sequences in bovine tissue. Hauswirth, W.W., Van de Walle, M.J., Laipis, P.J., Olivo, P.D. Cell (1984) [Pubmed]
  30. A stretch of "late" SV40 viral DNA about 400 bp long which includes the origin of replication is specifically exposed in SV40 minichromosomes. Varshavsky, A.J., Sundin, O., Bohn, M. Cell (1979) [Pubmed]
  31. Cloning of PI3 kinase-associated p85 utilizing a novel method for expression/cloning of target proteins for receptor tyrosine kinases. Skolnik, E.Y., Margolis, B., Mohammadi, M., Lowenstein, E., Fischer, R., Drepps, A., Ullrich, A., Schlessinger, J. Cell (1991) [Pubmed]
  32. The E. coli dnaY gene encodes an arginine transfer RNA. Garcia, G.M., Mar, P.K., Mullin, D.A., Walker, J.R., Prather, N.E. Cell (1986) [Pubmed]
  33. The DNA-binding domains of the jun oncoprotein and the yeast GCN4 transcriptional activator protein are functionally homologous. Struhl, K. Cell (1987) [Pubmed]
  34. Nucleotide sequence of the lexA gene of E. coli. Horii, T., Ogawa, T., Ogawa, H. Cell (1981) [Pubmed]
  35. A short nucleotide sequence required for regulation of HIS4 by the general control system of yeast. Donahue, T.F., Daves, R.S., Lucchini, G., Fink, G.R. Cell (1983) [Pubmed]
  36. Transcriptional activation by the Antennapedia and fushi tarazu proteins in cultured Drosophila cells. Winslow, G.M., Hayashi, S., Krasnow, M., Hogness, D.S., Scott, M.P. Cell (1989) [Pubmed]
  37. Nucleotide sequence of yeast LEU2 shows 5'-noncoding region has sequences cognate to leucine. Andreadis, A., Hsu, Y.P., Kohlhaw, G.B., Schimmel, P. Cell (1982) [Pubmed]
  38. Constitutively activated receptors for parathyroid hormone and parathyroid hormone-related peptide in Jansen's metaphyseal chondrodysplasia. Schipani, E., Langman, C.B., Parfitt, A.M., Jensen, G.S., Kikuchi, S., Kooh, S.W., Cole, W.G., Jüppner, H. N. Engl. J. Med. (1996) [Pubmed]
  39. 5' flanking region of immunoglobulin heavy chain constant region genes displays length heterogeneity in germlines of inbred mouse strains. Marcu, K.B., Banerji, J., Penncavage, N.A., Lang, R., Arnheim, N. Cell (1980) [Pubmed]
  40. Sequence analysis of adenovirus DNA: complete nucleotide sequence of the spliced 5' noncoding region of adenovirus 2 hexon messenger RNA. Akusjärvi, G., Pettersson, U. Cell (1979) [Pubmed]
  41. Studies of mouse mitochondrial DNA in Escherichia coli: structure and function of the eucaryotic-procaryotic chimeric plasmids. Chang, A.C., Lansman, R.A., Clayton, D.A., Cohen, S.N. Cell (1975) [Pubmed]
  42. Identification of rat gamma atrial natriuretic polypeptide and characterization of the cDNA encoding its precursor. Kangawa, K., Tawaragi, Y., Oikawa, S., Mizuno, A., Sakuragawa, Y., Nakazato, H., Fukuda, A., Minamino, N., Matsuo, H. Nature (1984) [Pubmed]
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