By Wolfsberg Tyra G., Wetterstrand Kris A., Guyer Mark S., Collins Francis S., Baxevanis Andreas D.
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Additional info for A user's guide to the human genome
6). In this section of the gene, the conserved mouse sequence overlaps with the exons. One way to retrieve sequence for a defined chromosomal region at the NCBI is with the seq link on the MapViewer, visible when the Gene_Seq map is the master (Fig. 2). At Ensembl, export genomic nucleotide sequence with the Export→FASTA link in any ContigView window (Fig. 14, center yellow bar). 6 supplement to nature genetics • september 2002 43 user’s guide Question 7 How would an investigator easily find compiled information describing the structure of a gene of interest?
10). The sequence corresponding to sequence 1 (the EST) is denoted as the query, whereas the sequence corresponding to sequence 2 (the known gene) is denoted as the subject. The known gene’s protein translation is also shown, starting at the end of the third row of the alignment. Examination of the alignment shows that the EST is missing 153 nt (nt 360–512 of the 34 mRNA), which corresponds to the fifth exon that is missing in BE798864. This gap is in frame, so the EST could encode a homologous yet shorter protein.
This does not mean, however, that the SNP marker necessarily falls within a coding region. If the C (for coding) appears in orange, part or all of the marker position overlaps with a coding region. The next column, labeled Het, indicates the average heterozygosity observed for this marker, on a scale of 0–100%. A reading of zero means that no information is available for that particular marker, whereas the pink bars show a 95% confidence interval for the marker. The Validation column indicates whether the marker has been validated (shown by a star) or is unvalidated (shown by light blue boxes).