colored red since these are “non-synonymous SNPs” – that is, the SNP produces a discrete change at the amino acid level. In contrast, consider the first set of green rows in the table, with the green indicating that this is a “synonymous SNP,” where the codons for the contig reference (G) and the SNP allele (A) ultimately produce the same amino acid (Glu); this is not altogether surprising, with the SNP being in the wobble position of the codon, where there is often redundancy in the genetic code. Additional information on human SNPs can be found in Chapter 15.
Figure 2.6 A section of the Database of Single Nucleotide Polymorphisms (dbSNP) GeneView page providing information on each SNP identified within the human DCC gene. See text for details.
Starting again from the Abstract view shown in Figure 2.3, protein sequences from RefSeq that have been linked to this abstract can be found by clicking on the Protein (RefSeq) link found in the Related information section on the right-hand side of the page, producing the view shown in Figure 2.7. Note that all but one of the entries is marked as “predicted”; the final entry in the list has an accession number beginning with NP, indicating that it contains an experimentally determined or verified sequence (see Box 1.2). Clicking on the first line of that entry (number 6) takes the user to the view shown in Figure 2.8, the RefSeq entry for the netrin receptor, the protein product of the DCC gene. The feature table – the section of the GenBank entry listing the location and characteristics of each of the documented biological features found within this protein sequence, such as post-translational modifications, recognizable repeat units, secondary structural regions, and clinically relevant variation – is particularly long in this case. This makes it difficult to determine the relative orientation of the features to one another and may lead the user to miss important interactions or relationships between biological features. Fortunately, a viewer that provides a bird's eye view of the elements found within the feature table is available by clicking on the Graphics link at the top of the entry, producing the more accessible display shown in Figure 2.9. Zoom controls are provided, and hovering over any of the elements in the display produces a pop-up containing the specific information for that feature from the GenBank entry.
Figure 2.7 Entries in the RefSeq protein database corresponding to the original Srour et al. (2010) entry in Figure 2.3. Entries can be accessed and examined by clicking on any of the accession numbers. See text for details.
Figure 2.8 The RefSeq entry for the netrin receptor, the protein product of the human DCC gene. The FASTA link at the top of the entry provides quick access to the protein sequence in FASTA format, while the Graphics link provides access to a graphical view of all of the individual elements captured within the entry's feature table (see Figure 2.9). See text for details.
Figure 2.9 The same RefSeq entry for the netrin receptor shown in Figure 2.8, now rendered in graphical format. The user can learn more about individual elements displayed in this view by simply hovering the cursor over any of the elements in the display; one such example is shown in the pop-up box at the bottom right, for the phosphorylation site at position 1267 of the sequence. Zoom and navigational controls are at the top of the view window, allowing the user to understand this gene within its broader genomic context.
From here, the user can also enter the structural realm by examining the protein structures that are available through the Discovery Column. Clicking on the See all 9 structures link takes the user to the view shown in Figure 2.10, listing structural entries related to the netrin receptor. The second entry is for the crystal structure of a fragment of netrin-1 complexed with the DCC receptor (PDB:4URT; Finci et al. 2014), and clicking on the title of that entry takes the user to the structure summary page shown in Figure 2.11. Starting on the right, the Interactions window shows the relationships between the individual elements in this biological unit, here consisting of the netrin-1 protein (circle A), the DCC receptor (circle B), and five different chemical entities (diamonds 1–5). The three-dimensional structure is shown in the left panel, and the structure can be further interrogated by clicking on the square with the diagonal arrow in the bottom left of that panel. This action will launch iCn3D (for “I see in three-D”), a web-based viewer that allows the structure to be rotated, provides coloring and rendering options to enhance visualization, and provides a wide variety of additional options; the reader is referred to the iCn3D online documentation for specifics. In the upper right of the 4URT structure summary page is a link to similar structures, as determined by VAST+. Clicking on the VAST+ link produces the output shown in Figure 2.12, here showing the first 10 of 256 structures deemed to have similar biological units to the query (4URT); the table shown here is sorted by RMSD of all aligned residues (in Å), from smallest to largest.
Figure 2.10 Protein structures associated with the RefSeq entry for the human netrin receptor shown in Figures 2.8 and 2.9. The description of each structure is hyperlinked, allowing the user to access the structure summary page for that entry (see Figure 2.11). Individual links below each entry allow quick access to related structures and proteins, information on conserved domains, and the iCn3D viewer.
