In the advanced search interface, we can see the search fields available in Gene if click on the “all fields” drop down (Figure 2 – a). Among the list of options are gene name and organism.
As an example, let’s search for the human
adenosine deaminase (ADA) gene.
To do this, we can use Gene’s advanced
search to make our search more specific.
NCBI Gene also provides the location and chromosomal coordinates of genes.
Each gene record within NCBI’s Gene database contains a gene model viewer showing models of transcripts, location of variants, etc. Information in the gene model viewer is organized into tracks. For instance, there is a transcript model track (Figure 6 – a). There is also a track indicating the location of the single nucleotide variants for the human ADA gene (Figure 6 – b). We can custom configure the tracks that are shown in the gene model viewer (more information in Figure 9).
Clicking on the “tools” tab (Figure 8 – a) will reveal an option to go to any location within the gene.
Recall from Figure 6 that the information in the gene model viewer are organized into tracks (i.e. transcript model track; variation track). We can custom configure the tracks that we want to see in the gene model viewer. To do this
If we click on the “ATG” tab (Figure 10 – a) in the gene model browser we can see the gene sequence overlaid on top of the transcript models (Figure 10 – b).
A very useful feature in the gene model viewer is the ability to view the amino acid translation of a particular gene in all six frames. We can configure the gene model viewer to show the six frame translation in the “configure page” dialogue box (refer to Figure 9 for instructions on accessing this box). In the “configure page” box, select sequence (Figure 11 – a). From there, scroll down the list of options and check the box that says “six-frame translations” (Figure 11 – b). Finally, hit the “configure tab” (Figure 11 – c).
The six-frame amino acid translation can inform us of locations for open reading frames (i.e. methionine pointed to by the red arrow in Figure 12). Note that the methionine pointed to by the red arrow in Figure 12 corresponds to the ATG start codon (red oval).
To download the sequence for a gene of interest, click on the “FASTA” tab on top of the gene model viewer (Figure 13 – a) and we will be directed to a page containing the gene sequence (human ADA gene in this example (Figure 14)).
After we have selected the region of the sequence that we want to download we can click on the “send to” tab (Figure 15 – a). From there select “complete record” (Figure 15 – b), choose file under “select destination” (Figure 15 – c), and select FASTA under format (Figure 15 – d). We can then finally hit “create file” (Figure 15 – e) and a file containing our gene interest will be downloaded. We can view this gene sequence in offline software such as UGENE (ugene.net).
To obtain exon coordinates from a gene record in the NCBI Gene database, click on the “full report” tab on the top left-hand corner of the gene record (Figure 16 – a). From the list of options, select “gene table (Figure 16 – b) and we will be directed to a page containing exon tables for all of the documented transcript variants (Figure 17).
In the exon table note that there is a column labeled “exon”. This column shows the coordinates for the exons appearing in the particular mRNA transcript. The column labeled “coding” are coordinates for the exons that are translated into protein.