Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2021 Nov 17;50(D1):D970–D979. doi: 10.1093/nar/gkab1005

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

PMC Copyright notice

Figure 2. — The Echinobase Gene Page. The top section of the page contains species agnostic information such as gene symbols, names and functions. It also contains synonyms, where legacy symbols and short names are stored and make genes locatable via database searches. The synonyms are also used to link Gene Pages to matched terms in the literature section. Due to the large amount of content aggregated on Gene Pages, much of the data is sorted into ‘tabs’ at the top of the page (orange arrow). Where a tab contains content, this is indicated by a numeral or icon. A transcriptional profile for the gene is also present, currently only for S. purpuratus, and will be expanded to additional species as data becomes available. The species specific content is arranged in vertical columns, each topped by a drop down menu that enables the user to define the content of that column (red arrow). In this example the third column header has been selected, displaying the three options for its content. The ‘+’ symbol highlighted by the green arrow allows additional columns to be displayed. As we will be adding both a fourth species and paralogs to the display options in the near future, the ability to customize the data viewed will become even more important. Where we store and integrate multiple genome versions, for example for S. purpuratus, the user can also select which genome version is displayed as a gene model via a drop-down menu, and which genome version is linked to the Gene Page in JBrowse. This is only the case when we have integrated multiple versions, and this is only the case in some species. As different genome builds (e.g. S. purpuratus v3.1 and v5.0) have different sets of gene models, not all genes will be available in all genome versions. When this happens the number of available genomes will change in the user display. The chromosome maps and gene model exon/intron graphics are generated dynamically from database content by JavaScript, and selecting a new genome version will dynamically display the new gene structure for the selected version. The rocket icon that appears adjacent to many sequence based hyperlinks will load the corresponding sequence into BLAST, while the magnifying glass icon will open the sequence in a display window.