Basic Information

This section is similar as that in gene profiles page. Here transcript sequence, CDS sequence and protein sequence could be viewed (≤ 10kb) and download.

DNA/Protein Statistics

This section shows some statistics based on this DNA/Protein sequences.

CDS Statistics

This section displays the base composition (A, T, G, C and sometimes the ambiguous N) of the CDS sequence.

Protein Statistics

This section displays several protein property statistics based on the protein sequence.

Exon-Intron Structure

This section displays the Exon-Intron structure in a table similar as the Ensembl database.

Exon-Intron Structure Table

This table consists of 10 columns:

• ID: We order all the segments of CDS, intron, UTR and surround sequences in the feature strand order. Clicking on the ID hyperlink would turn to the relevant region in JBrowse.
• Type: Possible values are: CDS, intron, UTR5 and UTR3.
• Chromosome, Start, End and Strand
• Phase: The 3' end phase for CDS segments.
• Length: The length (bp) of this segment.
• Sequence: Upper case for UTR/CDS and Lower case for intron or upstream/downstream region. In the table, upstream/downstream sequences are shown ≤ 50 bases, and intron sequences are shown ≤ 25 bases in both 5' and 3' end. Users can click the Download button to download full length sequences.

Download Sequence

Clicking the Download button would generate a text file containing the separated and combined sequences for all the segments. The region length of upstream/downstream could be customized.

Protein Domain

This section displays associated protein domains. Different domains are grouped by their databases and can be viewed by clicking the leading list.

Domain View

The domain region is visualized by the FeatureViewer plugin. Clicking the top-right help icon to get usage.

Homology

This section displays best homologs in other plant species.

Orthologs Among Other Plants

This section displays best orthologs in other cotton species and 22 other representative plant species. Data of most plant species are from Phytozome, and the detailed information of each hit gene could be accessed by attached hyperlinks.

Users can select some (or all) genes in this table and draw a Multiple Sequence Alignment Figure (Fig. 1). It is rendered by the MSA plugin. Users can sort, edit and download the alignment using relevant menus.

Fig 1. Select ortholog genes and draw multiple sequence alignment.

Cross Database References

This section gives a link to the Plant Homology Database if this transcript has ortholog in Arabidopsis thaliana.

Function

This section displays associated Gene Ontology, IntroPro and Pathway information . It would display functional annotation data from multiple sources (Fig. 2).

Fig 2. Example of multiple data sources of GO and InterPro annotations for gene Gh_A01G0139.1.

Gene Ontology Terms

CottonFGD uses the AmiGO service to visualize the relationship between the annotated GO item and its parents/children. GO items related to this transcript are highlighted. See Fig. 3A for a single GO item and Fig. 3B for multiple GO items.

Fig 3. Gene Ontology relationship visualization. A) a single GO item (Gh_A01G0005.1); B) multiple GO items (Gh_A01G0033.1)

Pathway Terms

CottonFGD uses the KEGG website to visualize the relationship between this transcript and its associated pathway. In the pathway figure, the target transcript is marked in red (Fig. 4).

Large pathways (with ≥ 200 items) are not visualized as they are mainly macro pathways (for example, ko01100) and are not related to specific biological process.

Fig 4. Pathway visualization.

Expression

The expression data of this transcript is grouped by experiment sets similar as the domain page.