The Browser View is the default page returned for your query(supported format). It displays gene and HCNE content in a GRB/ancient synteny block for all selected species in reference genome coordinates.
The gene and HCNE content for each species are listed as a vertical alignment in the order of evolutionary distance, with the reference genome listed first. Alternating background color serves as a visual delimiter between species.
The alignment is anchored by orthologous genes. For the reference species view, the coordinates for each feature are drawn to scale according to their genome coordinates; for all other species, each feature is placed based on the position of its reference species ortholog.
Below is an example search result page for PAX6, along with brief explanations of the various types of information that you can find there.
| A. | Synorth navigation bar Click the link for the Synorth view you want to use. You can view the GRB evolutionary scenarios in Locus Browser, Table Browser, or Tree Browser. The Locus Browser is shown above. |
| B. | Search field To view a GRB on Synorth, just type in your query gene symbol in supported formats, then hit "Enter" or click the "Search" button. |
| C. | Outlinks View the same region in other browsers (Ancora, UCSC Genome Browser, Ensembl and Vista). |
| D. | GRB coordinates This coordinate interval is a union of all synteny regions overlapping with your query gene, and is the region shown in the browser. If there is no synteny block-overlapping region was found, it will be empty. |
| E. | Track of Reference Species The track for reference species, which coordinate is scaled to the real coordinate in the reference genome. |
| F. | Track(s) of compared species These are tracks for compared species, each with an alternative background color. In each track, the species name and the sub-tracks for all synteny regions are shown. The first sub-track is the synteny region with most orthologous genes inside, the second contains the next-most features, and so on down the list. By default, only the sub-tracks from the smart mode will be displayed. |
| J1. | Gene Click a gene model to see gene informaiton in UCSC Genome Browser gene page(e.g. PAX6). |
| J2. | HCNE The HCNE track. |
| J3. | Fish-synteny region (FSR) The coordinate of syntenic region in the compared fish. |
| J4. | Outlink to other browser for FSR Click to see the fish-synteny region in other browser (A: Ancora; U: UCSC Genome Browser; E: Ensembl; V: Vista) |
| J5. | Sub-track for orthologous genes Show the orthologous genes in the given FSR, positioned vertically aligned to the ortholog gene in reference species. |
| J6. | Sub-track for HCNEs Show all HCNEs in that FSR, positioned vertically aligned to the coordinate in reference species. |
| J7. | Toggle trakcs Click to display/hide the sub-tracks. By default, it's controlled by the smart mode. |
| G. | Browser Legend Legend for the distinguished model in the browser. |
| H. | Chromosome Color Key Based on the UCSC Genome Browser's chromosome coloring schema. Only used for the compared species. |