International Nucleotide

Figure 15.4 Postsynthetic labeling of internal nucleotides in RNA. (A) Reaction of a nitroxide containing an aliphatic isocyanate with 2,-amino groups in RNA. (B) Reaction of methanethiosulfonate nitroxide with a 4-thiouridine nucleotide in RNA. (C) Reaction ofiodomethyl nitroxide with deoxyribo-phosphorothiolate linkage in RNA.

GenBank is the NIH genetic sequence database, and an annotated collection of all publicly available DNA sequences. It is part of the International Nucleotide Sequence Database Collaboration, which comprises the GenBank at NCBI, DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL). These three organizations exchange data on a daily basis. 

The important DNA sequence data repositories as the primary resources known as International Nucleotide Sequence Database Collaboration are ... 

International Nucleotide Sequence Database. URL http // www.ddbj.nig.ac.jp/. A joint compilation of heterogeneous sequence data into a redundant database. New and updated data shared daily by DNA Database of Japan (DDBJ). European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBD- Cambridge, U.K. URL http // www.ebi.ac.uk/Databases/. GenBank. NCBI. URL http // www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html. 

GenBank, EMBL, and DDBJ form the International Nucleotide Sequence Database Collaboration. The partnership databases are the richest source of publicly available annotated nucleotide sequences. The FT describes the features and syntax [28]. Although not all features involve patterns, many do. Examples include... 

Recently, the members of the International Nucleotide Sequence Database Collaboration (GenBank, EMBL, and DDBJ) introduced a better sequence identifier, one that combines an accession (which identifies a particular sequence record) with a version number (which tracks changes to the sequence itself). It is expected that this kind of Seq-id will become the preferred method of citing sequences. 

A full release of GenBank occins on a bimonthly schedule with incremental (and nonincremental) daily updates available by anonymous FTP. The International Nucleotide Sequence Database Collaboration also exchanges new and updated records daily. Therefore, all sequences present in GenBank are also present in DDBJ and EMBL, as described in the introduction to this chapter. The three databases rely on a common data format for information described in the feature table documentation (see below). This represents the lingua franca for nucleotide sequence database annotations. Together, the nucleotide sequence databases have developed defined submission procedures (see Chapter 4), a series of guidelines for the content and format of all records. 

This example also illustrates the use of the database cross-reference (db xref). This controlled qualiher allows the databases to cross-reference the sequence in question to an external database (the first identifier) with an identifier used in that database. The list of allowed db xref databases is maintained by the International Nucleotide Sequence Database Collaboration. 

Nucleic acid sequence databases typically contain sequence data, which includes information at the level of the gene structures, introns and exons (for eukaryotics), cDNA (complementary DNA), RNA and transcription regulations. The important nucleic acid sequence data repositories as the primary resources known as International Nucleotide Sequence Database Collaboration (INSDC) are ... 

INSDC International Nucleotide Sequence Database Collaboration... 

The partners of the International Nucleotide Sequence Databases (INSD), namely GenBank, EMBL, and DDBJ, share their nucleic acid... 

The evidence that VPg is linked to the 5 end of virion ENA rather than internally can be summarized as follows (i) Digestion of virion MA with Mase T2 yields VPg-pUp containing two phosphates, whereas digestion of virion RNA with nuclease PI yields Pg-pU containing only one phosphate. This observation is compatible only with VPg being linked to a 5 - terminal phosphate of uridine and not to an internal nucleotide (13)> (ii) Visualization of the protein... 

The incorporation of labeled amino acids by isolated nuclei from calf th3onus has been studied in detail by Allfrey and co-workers 1 4), and also by Breitman and Webster 66), and by Hopkins 1 4)- Nuclei from the thymus of puppies 67), from rabbit appendix 68), from chicken kidneys l 4)t from rat liver 69), from a lymphoma 64), and from wheat germ 70) have also been studied in this respect. The incorporation of labeled amino acids into the nuclear proteins is dependent on the presence of Na+ (the microsomal system requires K+) and upon oxidative phosphorylation. No effect of added amino acids or ATP have been demonstrated, but when the nuclei lose the ability to synthesize ATP from AMP, they also lose the ability to incorporate amino acids 71)-, however, they cannot utilize AMP supplied by the incubation medium, which means that they have to be prepared so as to retain their internal nucleotide pool. Amino acid incorporation also seems to be dependent upon a preliminary synthesis of RNA, since it is completely abolished by benzimidazole derivatives which inhibit the s3mthesis of the latter. However, intact RNA does not seem to be needed, and treatment with ribonuclease actually enhances amino acid incorporation into protein 7 ). 

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