GenBank accession codes

Biological raw data are stored in public databanks (such as Genbank or EMBL for primary DNA sequences). The data can be submitted and accessed via the World Wide Web. Protein sequence databanks like trEMBL provide the most likely translation of all coding sequences in the EMBL databank. Sequence data are prominent, but also other data are stored, e.g.yeast two-hybrid screens, expression arrays, systematic gene-knock-out experiments, and metabolic pathways. 

Pmrl (for plasma-membrane ATPase-related) of Saccharomyces cerevisiae was the first intracellular Ca2+-ATPase that was identified as a member of the SPCA family (Rudolph et al., 1989 Antebi and Fink, 1992 Sorin et al 1997). There are no introns in the coding region, like for most genes in S. cerevisiae. The Pmrl protein (GenBank accession no. AAA34884) comprises of 950 amino acids and has a molecular weight of 104 kDa. 

Figure 6. The cDNA structure of the human ISYNA1 gene. The gene encodes a 1676 bp coding region with a 5 UTR (untranslated region) of 50 bp and a 3 UTR of 98 bp (GenBank Accession AF220530).

The National Institutes of Health maintains a databank called Genbank, Its address on the internet is http / /www.ncbi.njm.nih gov. Once the homepage has been displayed on the screen, one can highlight Nucleotide Sequence Search, type the name of the protein coded by the nucleotides, and access the nucleotide sequence. Alternatively, one can highlight Protein Sequence Search, type the name of the protein, and acquire the amino acid sequence. If one knows the partial DNA sequence, i e, about 50 consecutive nucleotides, one can enter the sequence and, in this way, acquire a display of any gene that contains the entered sequence. If one knows the partial amino acid sequence, i.e., about 15 consecutive amino adds, one can also enter this sequence and get a display of any polypeptide containing the entered sequence. 

Fig. 1. Main window of the software package ANACONDA for two-codon context analysis at the ORFeome map level. The left panel presents a hierarchical tree of all genomes under analysis by ANACONDA. The Tab Valid includes all individual ORFs used to determine context bias and to build the respective map, whereas the Tab Reject allows visual inspection of ORFs that do not comply with the criteria selected during the opening of the ORFeome. An ORFeomic map for two-codon context bias obtained with the total set of predicted coding sequences of Thermotoga maritima (accession number AE000512 from GenBank), is shown.

Loader NM. Woolner EM. Hellyer A. Slabas AR. Safford R. Isolation and characterization of two Brassica napus embryo acyl-ACP thioesterase cDNA clones. Plant Mol Biol 1993 23 769-778. Dormann P. KridI JC. Ohirogge JB. Cloning and expression in Escherichia coli of a cDNA coding for the oleoyl-acyl carrier protein thioesterase from coriander seed endosperm (Plant Gene Register). Genbank accession number L20978. 

---